Package 'BASiCS'

Title:	Bayesian Analysis of Single-Cell Sequencing data
Description:	Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.
Authors:	Catalina Vallejos [aut, cre] , Nils Eling [aut], Alan O'Callaghan [aut], Sylvia Richardson [ctb], John Marioni [ctb]
Maintainer:	Catalina Vallejos <[email protected]>
License:	GPL-3
Version:	2.19.0
Built:	2024-10-30 04:22:12 UTC
Source:	https://github.com/bioc/BASiCS

Help Index

Generate balanced subsets for divide and conquer BASiCS
Methods for subsetting BASiCS_Result and BASiCS_ResultsDE objects.
Converting BASiCS results objects to data.frames
Convert concentration in moles per microlitre to molecule counts
The BASiCS_Chain class
'show' method for BASiCS_Chain objects
Remove global mean expression offset
Calculates denoised expression expression counts
Calculates denoised expression rates
Detection method for highly (HVG) and lowly (LVG) variable genes
Create diagnostic plots of MCMC parameters
Create diagnostic plots of MCMC parameters
Run divide and conquer MCMC with BASiCS
Generate a draw from the posterior of BASiCS using the generative model.
Calculate effective sample size for BASiCS_Chain parameters
Filter for input datasets
Loads pre-computed MCMC chains generated by the BASiCS_MCMC function
BASiCS MCMC sampler
Create a mock SingleCellExperiment object.
Produce plots assessing differential expression results
Visualise global offset in mean expression between two chains.
Plot variance decomposition results.
Plots of HVG/LVG search.
Prior parameters for BASiCS_MCMC
The BASiCS_Result class
The BASiCS_ResultDE class
The BASiCS_ResultsDE class
The BASiCS_ResultVG class
Plotting the trend after Bayesian regression
Generates synthetic data according to the model implemented in BASiCS
The BASiCS_Summary class
'show' method for BASiCS_Summary objects
Detection of genes with changes in expression
Decomposition of gene expression variability according to BASiCS
Detection method for highly and lowly variable genes using a grid of variance contribution thresholds
Defunct functions in package ‘BASiCS’
Extract from the chain obtained for the Grun et al (2014) data: pool-and-split samples
Extract from the chain obtained for the Grun et al (2014) data: pool-and-split samples (regression model)
Extract from the chain obtained for the Grun et al (2014) data: single-cell samples
Extract from the chain obtained for the Grun et al (2014) data: single-cell samples (regression model)
'dim' method for BASiCS_Chain objects
'dimnames' method for BASiCS_Chain objects
Accessors for the slots of a BASiCS_Chain object
Accessors for the slots of a BASiCS_Summary object
Methods for formatting BASiCS_Result and BASiCS_ResultsDE objects.
Create a synthetic SingleCellExperiment example object with the format required for BASiCS
Creates a BASiCS_Chain object from pre-computed MCMC chains
Creates a SingleCellExperiment object from a matrix of expression counts and experimental information about spike-in genes
'plot' method for BASiCS_Chain objects
'plot' method for BASiCS_Summary objects
rowData getter and setter for BASiCS_ResultsDE and BASiCS_ResultVG objects.
Accessors for the slots of a BASiCS_ResultDE object
Accessors for the slots of a BASiCS_ResultsDE object
Accessors for the slots of a BASiCS_ResultVG object
A 'subset' method for 'BASiCS_Chain“ objects
'Summary' method for BASiCS_Chain objects

Generate balanced subsets for divide and conquer BASiCS

Description

Partitions data based on either cells or genes. Attempts to find a partitioning scheme which is "balanced" for either total reads per cell across all genes (partitioning by gene) or total expression per gene across all cells (partitioning by gene). When partitioning by cell, at least 20 cells must be in each partition or BASiCS_MCMC will fail. If this partitioning fails, it will continue recursively up to a maximum number of iterations (20 by default).

Usage

.generateSubsets(
  Data,
  NSubsets,
  SubsetBy = c("cell", "gene"),
  Alpha = 0.05,
  WithSpikes = FALSE,
  MaxDepth = 20,
  .Depth = 1
)
.generateSubsets(
  Data,
  NSubsets,
  SubsetBy = c("cell", "gene"),
  Alpha = 0.05,
  WithSpikes = FALSE,
  MaxDepth = 20,
  .Depth = 1
)

Arguments

`Data`	a SingleCellExperiment object
`NSubsets`	Integer specifying the number of batches into which to divide Data for divide and conquer inference.
`SubsetBy`	Partition by "cell" or by "gene".
`Alpha`	p-value threshold for ANOVA testing of "balance"
`WithSpikes`	Similar to argument for BASiCS_MCMC - do the Data contain spikes?
`MaxDepth`	Maximum number of recursive
`.Depth`	Internal parameter. Do not set.

Value

A list of SingleCellExperiment objects

Methods for subsetting BASiCS_Result and BASiCS_ResultsDE objects.

Description

Methods for subsetting BASiCS_Result and BASiCS_ResultsDE objects.

Usage

## S4 method for signature 'BASiCS_ResultsDE,ANY,ANY,ANY'
x[i, j, drop = FALSE]

## S4 method for signature 'BASiCS_ResultsDE,ANY,ANY'
x[[i]]

## S4 method for signature 'BASiCS_Result,ANY,ANY,ANY'
x[i, j, drop = FALSE]
## S4 method for signature 'BASiCS_ResultsDE,ANY,ANY,ANY'
x[i, j, drop = FALSE]

## S4 method for signature 'BASiCS_ResultsDE,ANY,ANY'
x[[i]]

## S4 method for signature 'BASiCS_Result,ANY,ANY,ANY'
x[i, j, drop = FALSE]

Arguments

`x`	Object being subsetted.
`i`	See ?`[`, ?`[[`
`j`, `drop`	Ignored.

Value

An object of the same class as x.

Converting BASiCS results objects to data.frames

Description

Converting BASiCS results objects to data.frames

Usage

## S4 method for signature 'BASiCS_ResultsDE'
as.data.frame(x, Parameter, Filter = TRUE, ProbThreshold = NULL)

## S4 method for signature 'BASiCS_ResultDE'
as.data.frame(x, Filter = TRUE, ProbThreshold = NULL)

## S4 method for signature 'BASiCS_ResultVG'
as.data.frame(x, Filter = TRUE, ProbThreshold = NULL)
## S4 method for signature 'BASiCS_ResultsDE'
as.data.frame(x, Parameter, Filter = TRUE, ProbThreshold = NULL)

## S4 method for signature 'BASiCS_ResultDE'
as.data.frame(x, Filter = TRUE, ProbThreshold = NULL)

## S4 method for signature 'BASiCS_ResultVG'
as.data.frame(x, Filter = TRUE, ProbThreshold = NULL)

Arguments

`x`	An object of class BASiCS_ResultVG, BASiCS_ResultDE, or BASiCS_ResultsDE.
`Parameter`	For BASiCS_ResultsDE objects only. Character scalar specifying which table of results to output. Available options are "Mean", (mu, mean expression), "Disp" (delta, overdispersion) and "ResDisp" (epsilon, residual overdispersion).
`Filter`	Logical scalar. If `TRUE`, output only entries corresponding to genes that pass the decision rule used in the probabilistic test.
`ProbThreshold`	Only used if `Filter=TRUE`. Numeric scalar specifying the probability threshold to be used when filtering genes. Default is to use the threshold used in the original decision rule when the test was performed.

Value

A data.frame of test results.

Convert concentration in moles per microlitre to molecule counts

Description

Convert concentration in moles per microlitre to molecule counts

Usage

BASiCS_CalculateERCC(Mix, DilutionFactor, VolumePerCell)
BASiCS_CalculateERCC(Mix, DilutionFactor, VolumePerCell)

Arguments

`Mix`	The name of the spike-in mix to use.
`DilutionFactor`	The dilution factor applied to the spike-in mixture. e.g., 1 microlitre per 50ml would be a 1/50000 `DilutionFactor`.
`VolumePerCell`	The volume of spike-in mixture added to each well, or to each cell.

Value

The molecule counts per well, or per cell, based on the input parameters.

The BASiCS_Chain class

Description

Container of an MCMC sample of the BASiCS' model parameters as generated by the function BASiCS_MCMC.

Slots

parameters

List of matrices containing MCMC chains for each model parameter. Depending on the mode in which BASiCS was run, the following parameters can appear in the list:

mu: MCMC chain for gene-specific mean expression parameters $\mu_i$ , biological genes only (matrix with q.bio columns, all elements must be positive numbers)
delta: MCMC chain for gene-specific biological over-dispersion parameters $\delta_i$ , biological genes only (matrix with q.bio columns, all elements must be positive numbers)
phi: MCMC chain for cell-specific mRNA content normalisation parameters $\phi_j$ (matrix with n columns, all elements must be positive numbers and the sum of its elements must be equal to n)

This parameter is only used when spike-in genes are available.

s: MCMC chain for cell-specific technical normalisation parameters $s_j$ (matrix with n columns, all elements must be positive numbers)
nu: MCMC chain for cell-specific random effects $\nu_j$ (matrix with n columns, all elements must be positive numbers)
theta: MCMC chain for technical over-dispersion parameter(s) $\theta$ (matrix, all elements must be positive, each colum represents 1 batch)
beta: Only relevant for regression BASiCS model (Eling et al, 2017). MCMC chain for regression coefficients (matrix with k columns, where k represent the number of chosen basis functions + 2)
sigma2: Only relevant for regression BASiCS model (Eling et al, 2017). MCMC chain for the residual variance (matrix with one column, sigma2 represents a global parameter)
epsilon: Only relevant for regression BASiCS model (Eling et al, 2017). MCMC chain for the gene-specific residual over-dispersion parameter (matrix with q columns)
RefFreq: Only relevant for no-spikes BASiCS model (Eling et al, 2017). For each biological gene, this vector displays the proportion of times for which each gene was used as a reference (within the MCMC algorithm), when using the stochastic reference choice described in (Eling et al, 2017). This information has been kept as it is useful for the developers of this library. However, we do not expect users to need it.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


# A BASiCS_Chain object created by the BASiCS_MCMC function.
Data <- makeExampleBASiCS_Data()

# To run the model without regression
Chain <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2, Regression = FALSE)

# To run the model using the regression model
ChainReg <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2, Regression = TRUE)

# A BASiCS_Chain object created by the BASiCS_MCMC function.
Data <- makeExampleBASiCS_Data()

# To run the model without regression
Chain <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2, Regression = FALSE)

# To run the model using the regression model
ChainReg <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2, Regression = TRUE)

'show' method for BASiCS_Chain objects

Description

'show' method for BASiCS_Chain objects.

'updateObject' method for BASiCS_Chain objects. It is used to convert outdated BASiCS_Chain objects into a version that is compatible with the Bioconductor release of BASiCS. Do not use this method is BASiCS_Chain already contains a parameters slot.

Usage

## S4 method for signature 'BASiCS_Chain'
show(object)

## S4 method for signature 'BASiCS_Chain'
updateObject(object, ..., verbose = FALSE)
## S4 method for signature 'BASiCS_Chain'
show(object)

## S4 method for signature 'BASiCS_Chain'
updateObject(object, ..., verbose = FALSE)

Arguments

`object`	A `BASiCS_Chain` object.
`...`	Additional arguments of `updateObject` generic method. Not used within BASiCS.
`verbose`	Additional argument of `updateObject` generic method. Not used within BASiCS.

Value

Prints a summary of the properties of object.

Returns an updated BASiCS_Chain object that contains all model parameters in a single slot object (list).

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


Data <- makeExampleBASiCS_Data()
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 2, Burn = 2, Regression = FALSE)


# Not run
# New_Chain <- updateObject(Old_Chain)

Data <- makeExampleBASiCS_Data()
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 2, Burn = 2, Regression = FALSE)


# Not run
# New_Chain <- updateObject(Old_Chain)

Remove global mean expression offset

Description

Remove global offset in mean expression between two BASiCS_Chain objects.

Usage

BASiCS_CorrectOffset(Chain, ChainRef, min.mean = 1)
BASiCS_CorrectOffset(Chain, ChainRef, min.mean = 1)

Arguments

`Chain`	a 'BASiCS_MCMC' object to which the offset correction should be applied (with respect to 'ChainRef').
`ChainRef`	a 'BASiCS_MCMC' object to be used as the reference in the offset correction procedure.
`min.mean`	Minimum mean expression threshold required for inclusion in offset calculation. Similar to 'min.mean' in 'scran::computeSumFactors'.

Value

A list whose first element is an offset corrected version of 'Chain' (using 'ChainRef' as a reference), whose second element is the point estimate for the offset and whose third element contains iteration-specific offsets.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Alan O'Callaghan

Examples


# Loading two 'BASiCS_Chain' objects (obtained using 'BASiCS_MCMC')
data(ChainSC)
data(ChainRNA)

A <- BASiCS_CorrectOffset(ChainSC, ChainRNA)

# Offset corrected versions for ChainSC (with respect to ChainRNA). 
A$Chain
A$Offset

# Loading two 'BASiCS_Chain' objects (obtained using 'BASiCS_MCMC')
data(ChainSC)
data(ChainRNA)

A <- BASiCS_CorrectOffset(ChainSC, ChainRNA)

# Offset corrected versions for ChainSC (with respect to ChainRNA). 
A$Chain
A$Offset

Calculates denoised expression expression counts

Description

Calculates denoised expression counts by removing cell-specific technical variation. The latter includes global-scaling normalisation and therefore no further normalisation is required.

Usage

BASiCS_DenoisedCounts(Data, Chain, WithSpikes = TRUE)
BASiCS_DenoisedCounts(Data, Chain, WithSpikes = TRUE)

Arguments

`Data`	An object of class `SingleCellExperiment`
`Chain`	An object of class `BASiCS_Chain`
`WithSpikes`	A logical scalar specifying whether denoised spike-in genes should be generated as part of the output value. This only applies when the `BASiCS_Chain` object was generated with the setting `WithSpikes=TRUE`.

Details

See vignette browseVignettes("BASiCS")

Value

A matrix of denoised expression counts. In line with global scaling normalisation strategies, these are defined as $X_{ij}/(\phi_j \nu_j)$ for biological genes and $X_{ij}/(\nu_j)$ for spike-in genes. For this calculation $\phi_j$ $\nu_j$ are estimated by their corresponding posterior medians. If spike-ins are not used, $\phi_j$ is set equal to 1.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


Data <- makeExampleBASiCS_Data(WithSpikes = TRUE)
## The N and Burn parameters used here are optimised for speed
## and should not be used in regular use.
## For more useful parameters,
## see the vignette (\code{browseVignettes("BASiCS")})
Chain <- BASiCS_MCMC(Data, N = 1000, Thin = 10, Burn = 500,
                     Regression = FALSE, PrintProgress = FALSE)

DC <- BASiCS_DenoisedCounts(Data, Chain)

Data <- makeExampleBASiCS_Data(WithSpikes = TRUE)
## The N and Burn parameters used here are optimised for speed
## and should not be used in regular use.
## For more useful parameters,
## see the vignette (\code{browseVignettes("BASiCS")})
Chain <- BASiCS_MCMC(Data, N = 1000, Thin = 10, Burn = 500,
                     Regression = FALSE, PrintProgress = FALSE)

DC <- BASiCS_DenoisedCounts(Data, Chain)

Calculates denoised expression rates

Description

Calculates normalised and denoised expression rates, by removing the effect of technical variation.

Usage

BASiCS_DenoisedRates(Data, Chain, Propensities = FALSE)
BASiCS_DenoisedRates(Data, Chain, Propensities = FALSE)

Arguments

`Data`	an object of class `SingleCellExperiment`
`Chain`	an object of class `BASiCS_Chain`
`Propensities`	If `TRUE`, returns underlying expression propensitites $\rho_{ij}$ . Otherwise, denoised rates $\mu_i \rho_{ij}$ are returned. Default: `Propensities = FALSE`.

Details

See vignette

Value

A matrix of denoised expression rates (biological genes only)

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


Data <- makeExampleBASiCS_Data(WithSpikes = TRUE)
## The N and Burn parameters used here are optimised for speed
## and should not be used in regular use.
## For more useful parameters,
## see the vignette (\code{browseVignettes("BASiCS")})
Chain <- BASiCS_MCMC(Data, N = 1000, Thin = 10, Burn = 500,
                     Regression = FALSE, PrintProgress = FALSE)

DR <- BASiCS_DenoisedRates(Data, Chain)

Data <- makeExampleBASiCS_Data(WithSpikes = TRUE)
## The N and Burn parameters used here are optimised for speed
## and should not be used in regular use.
## For more useful parameters,
## see the vignette (\code{browseVignettes("BASiCS")})
Chain <- BASiCS_MCMC(Data, N = 1000, Thin = 10, Burn = 500,
                     Regression = FALSE, PrintProgress = FALSE)

DR <- BASiCS_DenoisedRates(Data, Chain)

Detection method for highly (HVG) and lowly (LVG) variable genes

Description

Functions to detect highly and lowly variable genes. If the BASiCS_Chain object was generated using the regression approach, BASiCS finds the top highly variable genes based on the posteriors of the epsilon parameters. Otherwise, the old approach is used, which initially performs a variance decomposition.

Usage

BASiCS_DetectVG(
  Chain,
  Task = c("HVG", "LVG"),
  PercentileThreshold = NULL,
  VarThreshold = NULL,
  ProbThreshold = 2/3,
  EpsilonThreshold = NULL,
  EFDR = 0.1,
  OrderVariable = c("Prob", "GeneIndex", "GeneName"),
  Plot = FALSE,
  MinESS = 100,
  ...
)

BASiCS_DetectLVG(Chain, ...)

BASiCS_DetectHVG(Chain, ...)
BASiCS_DetectVG(
  Chain,
  Task = c("HVG", "LVG"),
  PercentileThreshold = NULL,
  VarThreshold = NULL,
  ProbThreshold = 2/3,
  EpsilonThreshold = NULL,
  EFDR = 0.1,
  OrderVariable = c("Prob", "GeneIndex", "GeneName"),
  Plot = FALSE,
  MinESS = 100,
  ...
)

BASiCS_DetectLVG(Chain, ...)

BASiCS_DetectHVG(Chain, ...)

Arguments

`Chain`	an object of class `BASiCS_Chain`
`Task`	Search for highly variable genes (`Task="HVG"`) or lowly variable genes (`Task="LVG"`).
`PercentileThreshold`	Threshold to detect a percentile of variable genes (must be a positive value, between 0 and 1). Default: `PercentileThreshold = NULL`.
`VarThreshold`	Variance contribution threshold (must be a positive value, between 0 and 1). This is only used when the BASiCS non-regression model was used to generate the Chain object. Default: `VarThreshold = NULL`.
`ProbThreshold`	Optional parameter. Posterior probability threshold (must be a positive value, between 0 and 1). If `EFDR = NULL`, the posterior probability threshold for the test will be set to `ProbThreshold`.
`EpsilonThreshold`	Threshold for residual overdispersion above which
`EFDR`	Target for expected false discovery rate related to HVG/LVG detection. If `EFDR = NULL`, EFDR calibration is not performed and the posterior probability threshold is set equal to `ProbThreshold`. Default `EFDR = 0.10`.
`OrderVariable`	Ordering variable for output. Possible values: `'GeneIndex'`, `'GeneName'` and `'Prob'`. Default `ProbThreshold = 'Prob'`
`Plot`	If `Plot = TRUE` error control and expression versus HVG/LVG probability plots are generated.
`MinESS`	The minimum effective sample size for a gene to be included in the HVG or LVG tests. This helps to remove genes with poor mixing from detection of HVGs/LVGs. Default is 100. If set to NA, genes are not checked for effective sample size the tests are performed.
`...`	Graphical parameters (see `par`).

Details

In some cases, the EFDR calibration step may fail to find probability threshold that controls the EFDR at the chosen level. In cases like

See vignette

Value

An object of class BASiCS_ResultVG.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

Examples


# Loads short example chain (non-regression implementation)
data(ChainSC)

# Highly and lowly variable genes detection (within a single group of cells)
DetectHVG <- BASiCS_DetectHVG(ChainSC, VarThreshold = 0.60,
                              EFDR = 0.10, Plot = TRUE)
DetectLVG <- BASiCS_DetectLVG(ChainSC, VarThreshold = 0.40,
                              EFDR = 0.10, Plot = TRUE)
                              
# Loads short example chain (regression implementation)
data(ChainSCReg)

# Highly and lowly variable genes detection (within a single group of cells)
DetectHVG <- BASiCS_DetectHVG(ChainSCReg, PercentileThreshold = 0.90,
                              EFDR = 0.10, Plot = TRUE)
DetectLVG <- BASiCS_DetectLVG(ChainSCReg, PercentileThreshold = 0.10,
                              EFDR = 0.10, Plot = TRUE)

## Highly and lowly variable genes detection based on residual overdispersion
## threshold
DetectHVG <- BASiCS_DetectHVG(ChainSCReg, EpsilonThreshold = log(2), Plot = TRUE)
DetectLVG <- BASiCS_DetectLVG(ChainSCReg, EpsilonThreshold = -log(2), Plot = TRUE)

# Loads short example chain (non-regression implementation)
data(ChainSC)

# Highly and lowly variable genes detection (within a single group of cells)
DetectHVG <- BASiCS_DetectHVG(ChainSC, VarThreshold = 0.60,
                              EFDR = 0.10, Plot = TRUE)
DetectLVG <- BASiCS_DetectLVG(ChainSC, VarThreshold = 0.40,
                              EFDR = 0.10, Plot = TRUE)
                              
# Loads short example chain (regression implementation)
data(ChainSCReg)

# Highly and lowly variable genes detection (within a single group of cells)
DetectHVG <- BASiCS_DetectHVG(ChainSCReg, PercentileThreshold = 0.90,
                              EFDR = 0.10, Plot = TRUE)
DetectLVG <- BASiCS_DetectLVG(ChainSCReg, PercentileThreshold = 0.10,
                              EFDR = 0.10, Plot = TRUE)

## Highly and lowly variable genes detection based on residual overdispersion
## threshold
DetectHVG <- BASiCS_DetectHVG(ChainSCReg, EpsilonThreshold = log(2), Plot = TRUE)
DetectLVG <- BASiCS_DetectLVG(ChainSCReg, EpsilonThreshold = -log(2), Plot = TRUE)

Create diagnostic plots of MCMC parameters

Description

Plot a histogram of effective sample size or Geweke's diagnostic z-statistic. See effectiveSize and geweke.diag for more details.

Usage

BASiCS_DiagHist(
  object,
  Parameter = NULL,
  Measure = c("ess", "geweke.diag", "rhat"),
  VLine = TRUE,
  na.rm = TRUE
)

BASiCS_diagHist(...)
BASiCS_DiagHist(
  object,
  Parameter = NULL,
  Measure = c("ess", "geweke.diag", "rhat"),
  VLine = TRUE,
  na.rm = TRUE
)

BASiCS_diagHist(...)

Arguments

`object`	an object of class `BASiCS_Summary`
`Parameter`	Optional name of a chain parameter to restrict the histogram; if not supplied, all parameters will be assessed. Default `Parameter = NULL`.
`Measure`	Character scalar specifying the diagnostic measure to plot. Current options are effective sample size, the Geweke diagnostic criterion, and the `rhat` diagnostic.
`VLine`	Numeric scalar indicating a threshold value to be displayed as a dashed line on the plot. Alternatively, can be set to `FALSE` to disable line drawing, or `TRUE` to use the default thresholds.
`na.rm`	Logical scalar indicating whether NA values should be removed before calculating effective sample size.
`...`	Unused.

Value

A ggplot object.

Author(s)

Alan O'Callaghan

References

Geweke, J. Evaluating the accuracy of sampling-based approaches to calculating posterior moments. In _Bayesian Statistics 4_ (ed JM Bernado, JO Berger, AP Dawid and AFM Smith). Clarendon Press, Oxford, UK.

Examples


# Built-in example chain
data(ChainSC)

# See effective sample size distribution across all parameters
BASiCS_DiagHist(ChainSC)
# For mu only
BASiCS_DiagHist(ChainSC, Parameter = "mu")

# Built-in example chain
data(ChainSC)

# See effective sample size distribution across all parameters
BASiCS_DiagHist(ChainSC)
# For mu only
BASiCS_DiagHist(ChainSC, Parameter = "mu")

Create diagnostic plots of MCMC parameters

Description

Plot parameter values and effective sample size. See effectiveSize for more details on this diagnostic measure.

Usage

BASiCS_DiagPlot(
  object,
  Parameter = "mu",
  Measure = c("ess", "geweke.diag", "rhat"),
  x = NULL,
  y = NULL,
  LogX = isTRUE(x %in% c("mu", "delta")),
  LogY = isTRUE(y %in% c("mu", "delta")),
  Smooth = TRUE,
  HLine = TRUE,
  na.rm = TRUE
)

BASiCS_diagPlot(...)
BASiCS_DiagPlot(
  object,
  Parameter = "mu",
  Measure = c("ess", "geweke.diag", "rhat"),
  x = NULL,
  y = NULL,
  LogX = isTRUE(x %in% c("mu", "delta")),
  LogY = isTRUE(y %in% c("mu", "delta")),
  Smooth = TRUE,
  HLine = TRUE,
  na.rm = TRUE
)

BASiCS_diagPlot(...)

Arguments

`object`	an object of class `BASiCS_Summary`
`Parameter`	Name of the parameter to be plotted. Default `Parameter = 'mu'`
`Measure`	Character scalar specifying the diagnostic measure to plot. Current options are effective sample size, the Geweke diagnostic criterion, and the `rhat` diagnostic.
`x`, `y`	Optional MCMC parameter values to be plotted on the x or y axis, respectively. If neither is supplied, Parameter will be plotted on the x axis and effective sample size will be plotted on the y axis as a density plot.
`LogX`, `LogY`	A logical value indicating whether to use a log10 transformation for the x or y axis, respectively.
`Smooth`	A logical value indicating whether to use smoothing (specifically hexagonal binning using `geom_hex`).
`HLine`	Numeric scalar or vector indicating threshold value(s) to be displayed as a dashed line on the plot when `DrawHLine = TRUE`. Alternatively, can be set to `FALSE` to disable line drawing, or `TRUE` to use the default thresholds.
`na.rm`	Logical value indicating whether NA values should be removed before calculating effective sample size.
`...`	Unused.

Value

A ggplot object.

Author(s)

Alan O'Callaghan

Examples


# Built-in example chain
data(ChainSC)

# Point estimates versus effective sample size
BASiCS_DiagPlot(ChainSC, Parameter = "mu")
# Effective sample size as colour, mu as x, delta as y.
BASiCS_DiagPlot(ChainSC, x = "mu", y = "delta")

# Point estimates versus Geweke diagnostic
BASiCS_DiagPlot(ChainSC, Parameter = "mu", Measure = "geweke.diag")

# Built-in example chain
data(ChainSC)

# Point estimates versus effective sample size
BASiCS_DiagPlot(ChainSC, Parameter = "mu")
# Effective sample size as colour, mu as x, delta as y.
BASiCS_DiagPlot(ChainSC, x = "mu", y = "delta")

# Point estimates versus Geweke diagnostic
BASiCS_DiagPlot(ChainSC, Parameter = "mu", Measure = "geweke.diag")

Run divide and conquer MCMC with BASiCS

Description

Performs MCMC inference on batches of data. Data is divided into NSubsets batches, and BASiCS_MCMC is run on each batch separately.

Usage

BASiCS_DivideAndConquer(
  Data,
  NSubsets = 5,
  SubsetBy = c("cell", "gene"),
  Alpha = 0.05,
  WithSpikes,
  Regression,
  BPPARAM = BiocParallel::bpparam(),
  PriorParam = BASiCS_PriorParam(Data, PriorMu = "EmpiricalBayes"),
  RunName,
  StoreChains,
  StoreDir,
  Start,
  ...
)
BASiCS_DivideAndConquer(
  Data,
  NSubsets = 5,
  SubsetBy = c("cell", "gene"),
  Alpha = 0.05,
  WithSpikes,
  Regression,
  BPPARAM = BiocParallel::bpparam(),
  PriorParam = BASiCS_PriorParam(Data, PriorMu = "EmpiricalBayes"),
  RunName,
  StoreChains,
  StoreDir,
  Start,
  ...
)

Arguments

`Data`	SingleCellExperiemnt object
`NSubsets`	The number of batches to create and perform MCMC inference with.
`SubsetBy`	A character value specifying whether batches should consist of a subset of the cells in `Data` (when `SubsetBy="cell"`) or a subset of the genes in `Data` (when `SubsetBy="gene"`).
`Alpha`	A numeric value specifying the statistical significance level used to determine whether the average library size or average count are significantly different between batches.
`WithSpikes`, `Regression`, `PriorParam`	See `BASiCS_MCMC`.
`BPPARAM`	A `BiocParallelParam` instance.
`RunName`, `StoreChains`, `StoreDir`, `Start`	Unused. If used when calling this function, they are likely to result in undefined behaviour.
`...`	Passed to `BASiCS_MCMC`. All arguments required by `BASiCS_MCMC` must be supplied here, for example `N`, `Thin`, `Burn`.

Details

Subsets are chosen such that the average library size (when partitioning by cells) or average count (when partitioning by genes) is not significantly different between batches, at a significance level Alpha.

Value

A list of BASiCS_Chain objects.

References

Simple, Scalable and Accurate Posterior Interval Estimation Cheng Li and Sanvesh Srivastava and David B. Dunson arXiv (2016)

Examples

 bp <- BiocParallel::SnowParam()
 Data <- BASiCS_MockSCE()
 BASiCS_DivideAndConquer(
   Data, 
   NSubsets = 2,
   SubsetBy = "gene",
   N = 8,
   Thin = 2,
   Burn = 4,
   WithSpikes = TRUE,
   Regression = TRUE,
   BPPARAM = bp
 )
bp <- BiocParallel::SnowParam()
 Data <- BASiCS_MockSCE()
 BASiCS_DivideAndConquer(
   Data, 
   NSubsets = 2,
   SubsetBy = "gene",
   N = 8,
   Thin = 2,
   Burn = 4,
   WithSpikes = TRUE,
   Regression = TRUE,
   BPPARAM = bp
 )

Generate a draw from the posterior of BASiCS using the generative model.

Description

BASiCS_Draw creates a simulated dataset from the posterior of a fitted model implemented in BASiCS.

Usage

BASiCS_Draw(
  Chain,
  BatchInfo = gsub(".*_Batch([0-9a-zA-Z])", "\\1", colnames(Chain@parameters[["nu"]])),
  N = sample(nrow(Chain@parameters[["nu"]]), 1)
)
BASiCS_Draw(
  Chain,
  BatchInfo = gsub(".*_Batch([0-9a-zA-Z])", "\\1", colnames(Chain@parameters[["nu"]])),
  N = sample(nrow(Chain@parameters[["nu"]]), 1)
)

Arguments

`Chain`	An object of class `BASiCS_Chain`.
`BatchInfo`	Vector of batch information from the SingleCellExperiment object used as input to BASiCS_MCMC.
`N`	The integer index for the draw to be used to sample from the posterior predictive distribution. If not supplied, a random value is chosen.

Value

An object of class SingleCellExperiment, including synthetic data generated by the model implemented in BASiCS.

Author(s)

Alan O'Callaghan

References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

Examples

data(ChainSC)
BASiCS_Draw(ChainSC)

data(ChainSC)
BASiCS_Draw(ChainSC)

data(ChainSC)
BASiCS_Draw(ChainSC)

data(ChainSC)
BASiCS_Draw(ChainSC)

Calculate effective sample size for BASiCS_Chain parameters

Description

A function to calculate effective sample size BASiCS_Chain objects.

Usage

BASiCS_EffectiveSize(object, Parameter, na.rm = TRUE)

BASiCS_effectiveSize(...)
BASiCS_EffectiveSize(object, Parameter, na.rm = TRUE)

BASiCS_effectiveSize(...)

Arguments

`object`	an object of class `BASiCS_Chain`.
`Parameter`	The parameter to use to calculate effective sample size. Possible values: `'mu'`, `'delta'`, `'phi'`, `'s'`, `'nu'`, `'theta'`, `'beta'`, `'sigma2'` and `'epsilon'`.
`na.rm`	Remove `NA` values before calculating effective sample size. Only relevant when `Parameter = "epsilon"` (genes with very low expression are excluding when infering the mean/over-dispersion trend. Default: `na.rm = TRUE`.
`...`	Unused.

Value

A vector with effective sample sizes for all the elements of Parameter

Examples


data(ChainSC)
BASiCS_EffectiveSize(ChainSC, Parameter = "mu")

data(ChainSC)
BASiCS_EffectiveSize(ChainSC, Parameter = "mu")

Filter for input datasets

Description

BASiCS_Filter indicates which transcripts and cells pass a pre-defined inclusion criteria. The output of this function used to generate a SingleCellExperiment object required to run BASiCS. For more systematic tools for quality control, please refer to the scater Bioconductor package.

Usage

BASiCS_Filter(
  Counts,
  Tech = rep(FALSE, nrow(Counts)),
  SpikeInput = NULL,
  BatchInfo = NULL,
  MinTotalCountsPerCell = 2,
  MinTotalCountsPerGene = 2,
  MinCellsWithExpression = 2,
  MinAvCountsPerCellsWithExpression = 2
)
BASiCS_Filter(
  Counts,
  Tech = rep(FALSE, nrow(Counts)),
  SpikeInput = NULL,
  BatchInfo = NULL,
  MinTotalCountsPerCell = 2,
  MinTotalCountsPerGene = 2,
  MinCellsWithExpression = 2,
  MinAvCountsPerCellsWithExpression = 2
)

Arguments

`Counts`	Matrix of dimensions `q` times `n` whose elements corresponds to the simulated expression counts. First `q.bio` rows correspond to biological genes. Last `q-q.bio` rows correspond to technical spike-in genes.
`Tech`	Logical vector of length `q`. If `Tech = FALSE` the gene is biological; otherwise the gene is spike-in.
`SpikeInput`	Vector of length `q-q.bio` whose elements indicate the simulated input concentrations for the spike-in genes.
`BatchInfo`	Vector of length `n` whose elements indicate batch information. Not required if a single batch is present on the data. Default: `BatchInfo = NULL`.
`MinTotalCountsPerCell`	Minimum value of total expression counts required per cell (biological and technical). Default: `MinTotalCountsPerCell = 2`.
`MinTotalCountsPerGene`	Minimum value of total expression counts required per transcript (biological and technical). Default: `MinTotalCountsPerGene = 2`.
`MinCellsWithExpression`	Minimum number of cells where expression must be detected (positive count). Criteria applied to each transcript. Default: `MinCellsWithExpression = 2`.
`MinAvCountsPerCellsWithExpression`	Minimum average number of counts per cells where expression is detected. Criteria applied to each transcript. Default value: `MinAvCountsPerCellsWithExpression = 2`.

Value

A list of 2 elements

Counts: Filtered matrix of expression counts
Tech: Filtered vector of spike-in indicators
SpikeInput: Filtered vector of spike-in genes input molecules
BatchInfo: Filtered vector of the 'BatchInfo' argument
IncludeGenes: Inclusion indicators for transcripts
IncludeCells: Inclusion indicators for cells

Author(s)

Catalina A. Vallejos [email protected]

Examples


set.seed(1)
Counts <- matrix(rpois(50*10, 2), ncol = 10)
rownames(Counts) <- c(paste0('Gene', 1:40), paste0('Spike', 1:10))
Tech <- c(rep(FALSE,40),rep(TRUE,10))
set.seed(2)
SpikeInput <- rgamma(10,1,1)
SpikeInfo <- data.frame('SpikeID' = paste0('Spike', 1:10),
                        'SpikeInput' = SpikeInput)

Filter <- BASiCS_Filter(Counts, Tech, SpikeInput,
                        MinTotalCountsPerCell = 2,
                        MinTotalCountsPerGene = 2,
                        MinCellsWithExpression = 2,
                        MinAvCountsPerCellsWithExpression = 2)
SpikeInfoFilter <- SpikeInfo[SpikeInfo$SpikeID %in% rownames(Filter$Counts),]

set.seed(1)
Counts <- matrix(rpois(50*10, 2), ncol = 10)
rownames(Counts) <- c(paste0('Gene', 1:40), paste0('Spike', 1:10))
Tech <- c(rep(FALSE,40),rep(TRUE,10))
set.seed(2)
SpikeInput <- rgamma(10,1,1)
SpikeInfo <- data.frame('SpikeID' = paste0('Spike', 1:10),
                        'SpikeInput' = SpikeInput)

Filter <- BASiCS_Filter(Counts, Tech, SpikeInput,
                        MinTotalCountsPerCell = 2,
                        MinTotalCountsPerGene = 2,
                        MinCellsWithExpression = 2,
                        MinAvCountsPerCellsWithExpression = 2)
SpikeInfoFilter <- SpikeInfo[SpikeInfo$SpikeID %in% rownames(Filter$Counts),]

Loads pre-computed MCMC chains generated by the `BASiCS_MCMC` function

Description

Loads pre-computed MCMC chains generated by the BASiCS_MCMC function, creating a BASiCS_Chain object

Usage

BASiCS_LoadChain(RunName = "", StoreDir = getwd(), StoreUpdatedChain = FALSE)
BASiCS_LoadChain(RunName = "", StoreDir = getwd(), StoreUpdatedChain = FALSE)

Arguments

`RunName`	String used to index '.Rds' file containing the MCMC chain (produced by the `BASiCS_MCMC` function, with `StoreChains = TRUE`)
`StoreDir`	Directory where '.Rds' file is stored. Default: `StoreDir = getwd()`
`StoreUpdatedChain`	Only required when the input files contain an outdated version of a `BASiCS_Chain` object. If `StoreUpdatedChain = TRUE`, an updated object is saved (this overwrites original input file, if it was an '.Rds' file).

Value

An object of class BASiCS_Chain.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


Data <- makeExampleBASiCS_Data()
Chain <- BASiCS_MCMC(
  Data,
  N = 50,
  Thin = 5,
  Burn = 5,
  Regression = FALSE,
  StoreChains = TRUE,
  StoreDir = tempdir(),
  RunName = "Test"
)
ChainLoad <- BASiCS_LoadChain(RunName = "Test", StoreDir = tempdir())
Data <- makeExampleBASiCS_Data()
Chain <- BASiCS_MCMC(
  Data,
  N = 50,
  Thin = 5,
  Burn = 5,
  Regression = FALSE,
  StoreChains = TRUE,
  StoreDir = tempdir(),
  RunName = "Test"
)
ChainLoad <- BASiCS_LoadChain(RunName = "Test", StoreDir = tempdir())

BASiCS MCMC sampler

Description

MCMC sampler to perform Bayesian inference for single-cell mRNA sequencing datasets using the model described in Vallejos et al (2015).

Usage

BASiCS_MCMC(
  Data,
  N,
  Thin,
  Burn,
  Regression,
  WithSpikes = TRUE,
  PriorParam = BASiCS_PriorParam(Data, PriorMu = "EmpiricalBayes"),
  FixNu = FALSE,
  SubsetBy = c("none", "gene", "cell"),
  NSubsets = 1,
  CombineMethod = c("pie", "consensus"),
  Weighting = c("naive", "n_weight", "inverse_variance"),
  Threads = getOption("Ncpus", default = 1L),
  BPPARAM = BiocParallel::bpparam(),
  ...
)
BASiCS_MCMC(
  Data,
  N,
  Thin,
  Burn,
  Regression,
  WithSpikes = TRUE,
  PriorParam = BASiCS_PriorParam(Data, PriorMu = "EmpiricalBayes"),
  FixNu = FALSE,
  SubsetBy = c("none", "gene", "cell"),
  NSubsets = 1,
  CombineMethod = c("pie", "consensus"),
  Weighting = c("naive", "n_weight", "inverse_variance"),
  Threads = getOption("Ncpus", default = 1L),
  BPPARAM = BiocParallel::bpparam(),
  ...
)

Arguments

`Data`	A `SingleCellExperiment` object. If `WithSpikes = TRUE`, this MUST be formatted to include the spike-ins and/or batch information (see vignette).
`N`	Total number of iterations for the MCMC sampler. Use `N>=max(4,Thin)`, `N` being a multiple of `Thin`.
`Thin`	Thining period for the MCMC sampler. Use `Thin>=2`.
`Burn`	Burn-in period for the MCMC sampler. Use `Burn>=1`, `Burn<N`, `Burn` being a multiple of `Thin`.
`Regression`	If `Regression = TRUE`, BASiCS exploits a joint prior formulation for mean and over-dispersion parameters to estimate a measure of residual over-dispersion is not confounded by mean expression. Recommended setting is `Regression = TRUE`.
`WithSpikes`	If `WithSpikes = TRUE`, BASiCS will use reads from added spike-ins to estimate technical variability. If `WithSpikess = FALSE`, BASiCS depends on replicated experiments (batches) to estimate technical variability. In this case, please supply the BatchInfo vector in `colData(Data)`. Default: `WithSpikes = TRUE`.
`PriorParam`	List of prior parameters for BASiCS_MCMC. Should be created using `BASiCS_PriorParam`.
`FixNu`	Should the scaling normalisation factor `nu` be fixed to the starting value when `WithSpikes=FALSE`? These are set to scran scaling normalisation factors.
`SubsetBy`	Character value specifying whether a divide and conquer inference strategy should be used. When this is set to `"gene"`, inference is performed on batches of genes separately, and when it is set to `"cell"`, inference is performed on batches of cells separately. Posterior distributions are combined using posterior interval estimation (see Li et al., 2016).
`NSubsets`	If `SubsetBy="gene"` or `SubsetBy="cell"`, `NSubsets` specifies the number of batches to create and perform divide and conquer inference with.
`CombineMethod`	The method used to combine subposteriors if `SubsetBy` is set to `"gene"` or `"cell"`. Options are `"pie"` corresponding to posterior interval estimation (see Li et al., 2016) or `"consensus"` (see Scott et al., 2016). Both of these methods use a form of weighted average to combine subposterior draws into the final posterior.
`Weighting`	The weighting method used in the weighted average chosen using `CombineMethod`. Available options are `"naive"` (unweighted), `"n_weight"` (weights are chosen based on the size of each partition) and `"inverse_variance"` (subposteriors are weighted based on the inverse of the variance of the subposterior for each parameter).
`Threads`	Integer specifying the number of threads to be used to parallelise parameter updates. Default value is the globally set `"Ncpus"` option, or 1 if this option is not set.
`BPPARAM`	A `BiocParallelParam` instance, used for divide and conquer inference.
`...`	Optional parameters. `AR` Optimal acceptance rate for adaptive Metropolis Hastings updates. It must be a positive number between 0 and 1. Default (and recommended): `AR = 0.44`. `StopAdapt` Iteration at which adaptive proposals are not longer adapted. Use `StopAdapt>=1`. Default: `StopAdapt = Burn`. `StoreChains` If `StoreChains = TRUE`, the generated `BASiCS_Chain` object is stored as a '.Rds' file (`RunName` argument used to index the file name). Default: `StoreChains = FALSE`. `StoreAdapt` If `StoreAdapt = TRUE`, trajectory of adaptive proposal variances (in log-scale) for all parameters is stored as a list in a '.Rds' file (`RunName` argument used to index file name). Default: `StoreAdapt = FALSE`. `StoreDir` Directory where output files are stored. Only required if `StoreChains = TRUE` and/or `StoreAdapt = TRUE`. Default: `StoreDir = getwd()`. `RunName` String used to index '.Rds' files storing chains and/or adaptive proposal variances. `PrintProgress` If `PrintProgress = FALSE`, console-based progress report is suppressed. `Start` Starting values for the MCMC sampler. We do not advise to use this argument. Default options have been tuned to facilitate convergence. If changed, it must be a list containing the following elements: `mu0`, `delta0`, `phi0`, `s0`, `nu0`, `theta0`, `ls.mu0`, `ls.delta0`, `ls.phi0`, `ls.nu0` and `ls.theta0` `GeneExponent/CellExponent` Exponents applied to the prior for MCMC updates. Intended for use only when performing divide & conquer MCMC strategies.

Value

An object of class BASiCS_Chain.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

Vallejos, Richardson and Marioni (2016). Genome Biology.

Eling et al (2018). Cell Systems

Simple, Scalable and Accurate Posterior Interval Estimation Cheng Li and Sanvesh Srivastava and David B. Dunson arXiv (2016)

Bayes and Big Data: The Consensus Monte Carlo Algorithm Steven L. Scott, Alexander W. Blocker, Fernando V. Bonassi, Hugh A. Chipman, Edward I. George and Robert E. McCulloch International Journal of Management Science and Engineering Management (2016)

Examples


# Built-in simulated dataset
set.seed(1) 
Data <- makeExampleBASiCS_Data()
# To analyse real data, please refer to the instructions in:
# https://github.com/catavallejos/BASiCS/wiki/2.-Input-preparation

# Only a short run of the MCMC algorithm for illustration purposes
# Longer runs migth be required to reach convergence
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 2, Burn = 10, Regression = FALSE,
                     PrintProgress = FALSE, WithSpikes = TRUE)

# To run the regression version of BASiCS, use:
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 2, Burn = 10, Regression = TRUE,
                     PrintProgress = FALSE, WithSpikes = TRUE)

# To run the non-spike version BASiCS requires the data to contain at least
# 2 batches:
set.seed(2)
Data <- makeExampleBASiCS_Data(WithBatch = TRUE)
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 2, Burn = 10, Regression = TRUE,
                     PrintProgress = FALSE, WithSpikes = FALSE)

# For illustration purposes we load a built-in 'BASiCS_Chain' object
# (obtained using the 'BASiCS_MCMC' function)
data(ChainSC)

# `displayChainBASiCS` can be used to extract information from this output.
# For example:
head(displayChainBASiCS(ChainSC, Param = 'mu'))

# Traceplot (examples only)
plot(ChainSC, Param = 'mu', Gene = 1)
plot(ChainSC, Param = 'phi', Cell = 1)
plot(ChainSC, Param = 'theta', Batch = 1)

# Calculating posterior medians and 95% HPD intervals
ChainSummary <- Summary(ChainSC)

# `displaySummaryBASiCS` can be used to extract information from this output
# For example:
head(displaySummaryBASiCS(ChainSummary, Param = 'mu'))

# Graphical display of posterior medians and 95% HPD intervals
# For example:
plot(ChainSummary, Param = 'mu', main = 'All genes')
plot(ChainSummary, Param = 'mu', Genes = 1:10, main = 'First 10 genes')
plot(ChainSummary, Param = 'phi', main = 'All cells')
plot(ChainSummary, Param = 'phi', Cells = 1:5, main = 'First 5 cells')
plot(ChainSummary, Param = 'theta')

# To constrast posterior medians of cell-specific parameters
# For example:
par(mfrow = c(1,2))
plot(ChainSummary, Param = 'phi', Param2 = 's', SmoothPlot = FALSE)
# Recommended for large numbers of cells
plot(ChainSummary, Param = 'phi', Param2 = 's', SmoothPlot = TRUE)

# To constrast posterior medians of gene-specific parameters
par(mfrow = c(1,2))
plot(ChainSummary, Param = 'mu', Param2 = 'delta', log = 'x',
     SmoothPlot = FALSE)
# Recommended
plot(ChainSummary, Param = 'mu', Param2 = 'delta', log = 'x',
     SmoothPlot = TRUE)

# To obtain denoised rates / counts, see:
# help(BASiCS_DenoisedRates)
# and
# help(BASiCS_DenoisedCounts)

# For examples of differential analyses between 2 populations of cells see:
# help(BASiCS_TestDE)

# Built-in simulated dataset
set.seed(1) 
Data <- makeExampleBASiCS_Data()
# To analyse real data, please refer to the instructions in:
# https://github.com/catavallejos/BASiCS/wiki/2.-Input-preparation

# Only a short run of the MCMC algorithm for illustration purposes
# Longer runs migth be required to reach convergence
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 2, Burn = 10, Regression = FALSE,
                     PrintProgress = FALSE, WithSpikes = TRUE)

# To run the regression version of BASiCS, use:
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 2, Burn = 10, Regression = TRUE,
                     PrintProgress = FALSE, WithSpikes = TRUE)

# To run the non-spike version BASiCS requires the data to contain at least
# 2 batches:
set.seed(2)
Data <- makeExampleBASiCS_Data(WithBatch = TRUE)
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 2, Burn = 10, Regression = TRUE,
                     PrintProgress = FALSE, WithSpikes = FALSE)

# For illustration purposes we load a built-in 'BASiCS_Chain' object
# (obtained using the 'BASiCS_MCMC' function)
data(ChainSC)

# `displayChainBASiCS` can be used to extract information from this output.
# For example:
head(displayChainBASiCS(ChainSC, Param = 'mu'))

# Traceplot (examples only)
plot(ChainSC, Param = 'mu', Gene = 1)
plot(ChainSC, Param = 'phi', Cell = 1)
plot(ChainSC, Param = 'theta', Batch = 1)

# Calculating posterior medians and 95% HPD intervals
ChainSummary <- Summary(ChainSC)

# `displaySummaryBASiCS` can be used to extract information from this output
# For example:
head(displaySummaryBASiCS(ChainSummary, Param = 'mu'))

# Graphical display of posterior medians and 95% HPD intervals
# For example:
plot(ChainSummary, Param = 'mu', main = 'All genes')
plot(ChainSummary, Param = 'mu', Genes = 1:10, main = 'First 10 genes')
plot(ChainSummary, Param = 'phi', main = 'All cells')
plot(ChainSummary, Param = 'phi', Cells = 1:5, main = 'First 5 cells')
plot(ChainSummary, Param = 'theta')

# To constrast posterior medians of cell-specific parameters
# For example:
par(mfrow = c(1,2))
plot(ChainSummary, Param = 'phi', Param2 = 's', SmoothPlot = FALSE)
# Recommended for large numbers of cells
plot(ChainSummary, Param = 'phi', Param2 = 's', SmoothPlot = TRUE)

# To constrast posterior medians of gene-specific parameters
par(mfrow = c(1,2))
plot(ChainSummary, Param = 'mu', Param2 = 'delta', log = 'x',
     SmoothPlot = FALSE)
# Recommended
plot(ChainSummary, Param = 'mu', Param2 = 'delta', log = 'x',
     SmoothPlot = TRUE)

# To obtain denoised rates / counts, see:
# help(BASiCS_DenoisedRates)
# and
# help(BASiCS_DenoisedCounts)

# For examples of differential analyses between 2 populations of cells see:
# help(BASiCS_TestDE)

Create a mock SingleCellExperiment object.

Description

Creates a SingleCellExperiment object of Poisson-distributed approximating a homogeneous cell population.

Usage

BASiCS_MockSCE(
  NGenes = 100,
  NCells = 100,
  NSpikes = 20,
  WithBatch = TRUE,
  MeanMu = 1
)
BASiCS_MockSCE(
  NGenes = 100,
  NCells = 100,
  NSpikes = 20,
  WithBatch = TRUE,
  MeanMu = 1
)

Arguments

`NGenes`	Integer value specifying the number of genes that will be present in the output.
`NCells`	Integer value specifying the number of cells that will be present in the output.
`NSpikes`	Integer value specifying the number of spike-in genes that will be present in the output.
`WithBatch`	Logical value specifying whether a dummy `BatchInfo` is included in the output.
`MeanMu`	The log mean used to generate per-gene mean expression levels.

Value

A SingleCellExperiment object.

Examples

BASiCS_MockSCE()
BASiCS_MockSCE()

Produce plots assessing differential expression results

Description

Produce plots assessing differential expression results

Usage

BASiCS_PlotDE(object, ...)

## S4 method for signature 'BASiCS_ResultsDE'
BASiCS_PlotDE(
  object,
  Plots = c("MA", "Volcano", "Grid"),
  Parameters = intersect(c("Mean", "Disp", "ResDisp"), names(object@Results)),
  MuX = TRUE,
  ...
)

## S4 method for signature 'BASiCS_ResultDE'
BASiCS_PlotDE(
  object,
  Plots = c("Grid", "MA", "Volcano"),
  Mu = NULL,
  TransLogit = FALSE
)

## S4 method for signature 'missing'
BASiCS_PlotDE(
  GroupLabel1,
  GroupLabel2,
  ProbThresholds = seq(0.5, 0.9995, by = 0.00025),
  Epsilon,
  EFDR,
  Table,
  Measure,
  EFDRgrid,
  EFNRgrid,
  ProbThreshold,
  Mu,
  TransLogit = FALSE,
  Plots = c("Grid", "MA", "Volcano")
)
BASiCS_PlotDE(object, ...)

## S4 method for signature 'BASiCS_ResultsDE'
BASiCS_PlotDE(
  object,
  Plots = c("MA", "Volcano", "Grid"),
  Parameters = intersect(c("Mean", "Disp", "ResDisp"), names(object@Results)),
  MuX = TRUE,
  ...
)

## S4 method for signature 'BASiCS_ResultDE'
BASiCS_PlotDE(
  object,
  Plots = c("Grid", "MA", "Volcano"),
  Mu = NULL,
  TransLogit = FALSE
)

## S4 method for signature 'missing'
BASiCS_PlotDE(
  GroupLabel1,
  GroupLabel2,
  ProbThresholds = seq(0.5, 0.9995, by = 0.00025),
  Epsilon,
  EFDR,
  Table,
  Measure,
  EFDRgrid,
  EFNRgrid,
  ProbThreshold,
  Mu,
  TransLogit = FALSE,
  Plots = c("Grid", "MA", "Volcano")
)

Arguments

`object`	A BASiCS_ResultsDE or BASiCS_ResultDE object.
`...`	Passed to methods.
`Plots`	Plots plot to produce? Options: "MA", "Volcano", "Grid".
`Parameters`	Character vector specifying the parameter(s) to produce plots for, Available options are "Mean", (mu, mean expression), "Disp" (delta, overdispersion) and "ResDisp" (epsilon, residual overdispersion).
`MuX`	Use Mu (mean expression across both chains) as the X-axis for all MA plots? Default: TRUE.
`Mu`, `GroupLabel1`, `GroupLabel2`, `ProbThresholds`, `Epsilon`, `EFDR`, `Table`, `Measure`, `EFDRgrid`, `EFNRgrid`, `ProbThreshold`	Internal arguments.
`TransLogit`	Logical scalar controlling whether a logit transform is applied to the posterior probability in the y-axis of volcano plots. As logit(0) and logit(1) are undefined, we clip these values near the range of the data excluding 0 and 1.

Value

A plot (possibly several combined using plot_grid).

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Alan O'Callaghan

Examples

data(ChainSC)
data(ChainRNA)

Test <- BASiCS_TestDE(Chain1 = ChainSC, Chain2 = ChainRNA,
                      GroupLabel1 = 'SC', GroupLabel2 = 'P&S',
                      EpsilonM = log2(1.5), EpsilonD = log2(1.5),
                      OffSet = TRUE)
BASiCS_PlotDE(Test)
data(ChainSC)
data(ChainRNA)

Test <- BASiCS_TestDE(Chain1 = ChainSC, Chain2 = ChainRNA,
                      GroupLabel1 = 'SC', GroupLabel2 = 'P&S',
                      EpsilonM = log2(1.5), EpsilonD = log2(1.5),
                      OffSet = TRUE)
BASiCS_PlotDE(Test)

Visualise global offset in mean expression between two chains.

Description

Visualise global offset in mean expression between two BASiCS_Chain objects.

Usage

BASiCS_PlotOffset(
  Chain1,
  Chain2,
  Type = c("offset estimate", "before-after", "MAPlot"),
  GroupLabel1 = "Group 1",
  GroupLabel2 = "Group 2"
)
BASiCS_PlotOffset(
  Chain1,
  Chain2,
  Type = c("offset estimate", "before-after", "MAPlot"),
  GroupLabel1 = "Group 1",
  GroupLabel2 = "Group 2"
)

Arguments

`Chain1`, `Chain2`	BASiCS_Chain objects to be plotted.
`Type`	The type of plot generated. `"offset estimate"` produces a boxplot of the offset alongside an estimate of the global offset. `"before-after"` produces MA plots of Mean expression against log2(fold-change) before and after offset correction. `"MA plot"` produces an MA plot of Mean expression against log2(fold-change).
`GroupLabel1`, `GroupLabel2`	Labels for Chain1 and Chain2 in the resulting plot(s).

Value

Plot objects.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Alan O'Callaghan

Examples


# Loading two 'BASiCS_Chain' objects (obtained using 'BASiCS_MCMC')
data("ChainSC")
data("ChainRNA")

BASiCS_PlotOffset(ChainSC, ChainRNA)

# Loading two 'BASiCS_Chain' objects (obtained using 'BASiCS_MCMC')
data("ChainSC")
data("ChainRNA")

BASiCS_PlotOffset(ChainSC, ChainRNA)

Plot variance decomposition results.

Description

Plot variance decomposition results.

Usage

BASiCS_PlotVarianceDecomp(
  Decomp,
  beside = FALSE,
  nBatch = ((ncol(Decomp) - 2)/3) - 1,
  main = "Overall variance decomposition",
  xlabs = if (nBatch == 1) "Overall" else c("Overall", paste("Batch", seq_len(nBatch))),
  ylab = "% of variance"
)
BASiCS_PlotVarianceDecomp(
  Decomp,
  beside = FALSE,
  nBatch = ((ncol(Decomp) - 2)/3) - 1,
  main = "Overall variance decomposition",
  xlabs = if (nBatch == 1) "Overall" else c("Overall", paste("Batch", seq_len(nBatch))),
  ylab = "% of variance"
)

Arguments

`Decomp`	The output of `BASiCS_VarianceDecomp`.
`beside`	If `TRUE`, bars are placed beside each other. If `FALSE`, bars are stacked.
`nBatch`	Number of batches.
`main`	Plot title.
`xlabs`	x-axis labels. Defaults to "Batch 1", "Batch 2", etc.
`ylab`	y axis label.

Value

A ggplot object.

Plots of HVG/LVG search.

Description

Plots of HVG/LVG search.

Usage

BASiCS_PlotVG(object, Plot = c("Grid", "VG"), ...)
BASiCS_PlotVG(object, Plot = c("Grid", "VG"), ...)

Arguments

`object`	BASiCS_ResultVG object.
`Plot`	Character scalar specifying the type of plot to be made. Options are "Grid" and "VG".
`...`	Optional graphical parameters passed to `.VGPlot` (internal function).

Value

A plot.

Examples

data(ChainSC)

# Highly and lowly variable genes detection (within a single group of cells)
DetectHVG <- BASiCS_DetectHVG(ChainSC, VarThreshold = 0.60,
                              EFDR = 0.10, Plot = TRUE)
BASiCS_PlotVG(DetectHVG)
data(ChainSC)

# Highly and lowly variable genes detection (within a single group of cells)
DetectHVG <- BASiCS_DetectHVG(ChainSC, VarThreshold = 0.60,
                              EFDR = 0.10, Plot = TRUE)
BASiCS_PlotVG(DetectHVG)

Prior parameters for BASiCS_MCMC

Description

This is a convenience function to allow partial specification of prior parameters, and to ensure default parameters are consistent across usage within the package.

Usage

BASiCS_PriorParam(
  Data,
  k = 12,
  mu.mu = NULL,
  s2.mu = 0.5,
  s2.delta = 0.5,
  a.delta = 1,
  b.delta = 1,
  p.phi = rep(1, times = ncol(Data)),
  a.s = 1,
  b.s = 1,
  a.theta = 1,
  b.theta = 1,
  RBFMinMax = TRUE,
  FixLocations = !is.null(RBFLocations) | !is.na(MinGenesPerRBF),
  RBFLocations = NULL,
  MinGenesPerRBF = NA,
  variance = 1.2,
  m = numeric(k),
  V = diag(k),
  a.sigma2 = 2,
  b.sigma2 = 2,
  eta = 5,
  PriorMu = c("default", "EmpiricalBayes"),
  PriorDelta = c("log-normal", "gamma"),
  StochasticRef = TRUE,
  ConstrainProp = 0.2,
  GeneExponent = 1,
  CellExponent = 1
)
BASiCS_PriorParam(
  Data,
  k = 12,
  mu.mu = NULL,
  s2.mu = 0.5,
  s2.delta = 0.5,
  a.delta = 1,
  b.delta = 1,
  p.phi = rep(1, times = ncol(Data)),
  a.s = 1,
  b.s = 1,
  a.theta = 1,
  b.theta = 1,
  RBFMinMax = TRUE,
  FixLocations = !is.null(RBFLocations) | !is.na(MinGenesPerRBF),
  RBFLocations = NULL,
  MinGenesPerRBF = NA,
  variance = 1.2,
  m = numeric(k),
  V = diag(k),
  a.sigma2 = 2,
  b.sigma2 = 2,
  eta = 5,
  PriorMu = c("default", "EmpiricalBayes"),
  PriorDelta = c("log-normal", "gamma"),
  StochasticRef = TRUE,
  ConstrainProp = 0.2,
  GeneExponent = 1,
  CellExponent = 1
)

Arguments

`Data`	SingleCellExperiment object (required).
`k`	Number of regression terms, including k - 2 Gaussian radial basis functions (GRBFs).
`mu.mu`, `s2.mu`	Mean and variance parameters for lognormal prior on mu.
`s2.delta`	Variance parameter for lognormal prior on delta when `PriorDelta="lognormal"`.
`a.delta`, `b.delta`	Parameters for gamma prior on delta when `PriorDelta="gamma"`.
`p.phi`	Parameter for dirichlet prior on phi.
`a.s`, `b.s`	Parameters for gamma prior on s.
`a.theta`, `b.theta`	Parameters for gamma prior on theta.
`RBFMinMax`	Should GRBFs be placed at the minimum and maximum of `log(mu)`?
`FixLocations`	Should RBFLocations be fixed throughout MCMC, or adaptive during burn-in? By default this is `FALSE`, but it is set to `TRUE` if `RBFLocations` or `MinGenesPerRBF` are specified.
`RBFLocations`	Numeric vector specifying locations of GRBFs in units of `log(mu)`.
`MinGenesPerRBF`	Numeric scalar specifying the minimum number of genes for GRBFs to be retained. If fewer than `MinGenesPerRBF` genes have values of `log(mu)` within the range of an RBF, it is removed. The range covered by each RBF is defined as centre of the RBF plus or minus half the distance between RBFs.
`variance`	Variance of the GRBFs.
`m`, `V`	Mean and (co)variance priors for regression coefficients.
`a.sigma2`, `b.sigma2`	Priors for inverse gamma prior on regression scale.
`eta`	Degrees of freedom for t distribution of regresion errors.
`PriorMu`	Indicates if the original prior (`PriorMu = 'default'`) or an empirical Bayes approach (`PriorMu = 'EmpiricalBayes'`) will be assigned to gene-specific mean expression parameters.
`PriorDelta`	Scalar character specifying the prior type to use for delta overdispersion parameter. Options are "log-normal" (recommended) and "gamma" (used in Vallejos et al. (2015)).
`StochasticRef`	Logical scalar specifying whether the reference gene for the no-spikes version should be chosen randomly at MCMC iterations.
`ConstrainProp`	Proportion of genes to be considered as reference genes if `StochasticRef=TRUE`.
`GeneExponent`, `CellExponent`	Exponents for gene and cell-specific parameters. These should not be outside of divide and conquer MCMC applications.

Value

A list containing the prior hyper-parameters that are required to run the algoritm implemented in BASiCS_MCMC.

Examples


BASiCS_PriorParam(makeExampleBASiCS_Data(), k = 12)


BASiCS_PriorParam(makeExampleBASiCS_Data(), k = 12)

The BASiCS_Result class

Description

Container of results for a single test (HVG/LVG/DE). This should be an abstract class (but this is R so no) and shouldn't be directly instantiated. Defines a very small amount of common behaviour for BASiCS_ResultDE and BASiCS_ResultVG.

Slots

Table: Tabular results for each gene.
Name: The name of the test performed (typically "Mean", "Disp" or "ResDisp")
ProbThreshold: Posterior probability threshold used in differential test.
EFDR,EFNR: Expected false discovery and expected false negative rates for differential test.
Extra: Additional objects for class flexibility.

The BASiCS_ResultDE class

Description

Container of results for a single differential test.

Slots

Table: Tabular results for each gene.
Name: The name of the test performed (typically "Mean", "Disp" or "ResDisp")
GroupLabel1,GroupLabel2: Group labels.
ProbThreshold: Posterior probability threshold used in differential test.
EFDR,EFNR: Expected false discovery and expected false negative rates for differential test.
EFDRgrid,EFNRgrid: Grid of EFDR and EFNR values calculated before thresholds were fixed.
Epsilon: Minimum fold change or difference threshold.
Extra: objects for class flexibility.

The BASiCS_ResultsDE class

Description

Results of BASiCS_TestDE

Slots

Results: BASiCS_ResultDE objects
Chain1,Chain2: BASiCS_Chain objects.
GroupLabel1,GroupLabel2: Labels for Chain1 and Chain2
Offset: Ratio between median of chains
RowData: Annotation for genes
Extras: Slot for extra information to be added later

The BASiCS_ResultVG class

Description

Container of results for a single HVG/LVG test.

Slots

Method: Character value detailing whether the test performed using a threshold directly on epsilon values (Method="Epsilon"), variance decomposition (Method="Variance") or percentiles of epsilon (Method="Percentile").
RowData: Optional DataFrame containing additional information about genes used in the test.
EFDRgrid,EFNRgrid: Grid of EFDR and EFNR values calculated before thresholds were fixed.
Threshold: Threshold used to calculate tail posterior probabilities for the HVG or LVG decision rule.
ProbThresholds: Probability thresholds used to calculate EFDRGrid and EFNRGrid.
ProbThreshold: Posterior probability threshold used in the HVG/LVG decision rule.

Plotting the trend after Bayesian regression

Description

Plotting the trend after Bayesian regression using a BASiCS_Chain object

Usage

BASiCS_ShowFit(
  object,
  xlab = "log(mu)",
  ylab = "log(delta)",
  pch = 16,
  smooth = TRUE,
  variance = 1.2,
  colour = "dark blue",
  markExcludedGenes = TRUE,
  GenesSel = NULL,
  colourGenesSel = "dark red",
  Uncertainty = TRUE
)
BASiCS_ShowFit(
  object,
  xlab = "log(mu)",
  ylab = "log(delta)",
  pch = 16,
  smooth = TRUE,
  variance = 1.2,
  colour = "dark blue",
  markExcludedGenes = TRUE,
  GenesSel = NULL,
  colourGenesSel = "dark red",
  Uncertainty = TRUE
)

Arguments

`object`	an object of class `BASiCS_Chain`
`xlab`	As in `par`.
`ylab`	As in `par`.
`pch`	As in `par`. Default value `pch = 16`.
`smooth`	Logical to indicate wether the smoothScatter function is used to plot the scatter plot. Default value `smooth = TRUE`.
`variance`	Variance used to build GRBFs for regression. Default value `variance = 1.2`
`colour`	colour used to denote genes within the scatterplot. Only used when `smooth = TRUE`. Default value `colour = "dark blue"`.
`markExcludedGenes`	Whether or not lowly expressed genes that were excluded from the regression fit are included in the scatterplot. Default value `markExcludedGenes = TRUE`.
`GenesSel`	Vector of gene names to be highlighted in the scatterplot. Only used when `smooth = TRUE`. Default value `GenesSel = NULL`.
`colourGenesSel`	colour used to denote the genes listed in `GenesSel` within the scatterplot. Default value `colourGenesSel = "dark red"`.
`Uncertainty`	logical indicator. If true, statistical uncertainty around the regression fit is shown in the plot.

Value

A ggplot2 object

Author(s)

Nils Eling [email protected]

Catalina Vallejos [email protected]

References

Eling et al (2018). Cell Systems https://doi.org/10.1016/j.cels.2018.06.011

Examples

data(ChainRNAReg)
BASiCS_ShowFit(ChainRNAReg)

data(ChainRNAReg)
BASiCS_ShowFit(ChainRNAReg)

Generates synthetic data according to the model implemented in BASiCS

Description

BASiCS_Sim creates a simulated dataset from the model implemented in BASiCS.

Usage

BASiCS_Sim(Mu, Mu_spikes = NULL, Delta, Phi = NULL, S, Theta, BatchInfo = NULL)
BASiCS_Sim(Mu, Mu_spikes = NULL, Delta, Phi = NULL, S, Theta, BatchInfo = NULL)

Arguments

`Mu`	Gene-specific mean expression parameters $\mu_i$ for all biological genes (vector of length `q.bio`, all elements must be positive numbers)
`Mu_spikes`	$\mu_i$ for all technical genes defined as true input molecules (vector of length `q-q.bio`, all elements must be positive numbers). If `Mu_spikes = NULL`, the generated data will not contain spike-ins. If `Phi = NULL`, `Mu_spikes` will be ignored. Default: `Mu_spikes = NULL`.
`Delta`	Gene-specific biological over-dispersion parameters $\delta_i$ , biological genes only (vector of length `q.bio`, all elements must be positive numbers)
`Phi`	Cell-specific mRNA content normalising parameters $\phi_j$ (vector of length `n`, all elements must be positive numbers and the sum of its elements must be equal to `n`). `Phi` must be set equal to `NULL` when generating data without spike-ins. If `Mu_spikes = NULL`, `Phi` will be ignored. Default: `Phi = NULL`
`S`	Cell-specific technical normalising parameters $s_j$ (vector of length `n`, all elements must be positive numbers)
`Theta`	Technical variability parameter $\theta$ (must be positive). `Theta` can be a scalar (single batch of samples), or a vector (multiple batches of samples). If a value for `BatchInfo` is provided, the length of `Theta` must match the number of unique values in `BatchInfo`.
`BatchInfo`	Vector detailing which batch each cell should be simulated from. If spike-ins are not in use, the number of unique values contained in `BatchInfo` must be larger than 1 (i.e. multiple batches are present).

Value

An object of class SingleCellExperiment, including synthetic data generated by the model implemented in BASiCS.

Author(s)

Catalina A. Vallejos [email protected], Nils Eling

References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

Examples


# Simulated parameter values for 10 genes
# (7 biogical and 3 spike-in) measured in 5 cells
Mu <- c(8.36, 10.65, 4.88, 6.29, 21.72, 12.93, 30.19)
Mu_spikes <-  c(1010.72, 7.90, 31.59)
Delta <- c(1.29, 0.88, 1.51, 1.49, 0.54, 0.40, 0.85)
Phi <- c(1.00, 1.06, 1.09, 1.05, 0.80)
S <- c(0.38, 0.40, 0.38, 0.39, 0.34)
Theta <- 0.39

# Data with spike-ins, single batch
Data <- BASiCS_Sim(Mu, Mu_spikes, Delta, Phi, S, Theta)
head(SingleCellExperiment::counts(Data))
dim(SingleCellExperiment::counts(Data))
altExp(Data)
rowData(altExp(Data))

# Data with spike-ins, multiple batches
BatchInfo <- c(1,1,1,2,2)
Theta2 <- rep(Theta, times = 2)
Data <- BASiCS_Sim(Mu, Mu_spikes, Delta, Phi, S, Theta2, BatchInfo)

# Data without spike-ins, multiple batches
Data <- BASiCS_Sim(Mu, Mu_spikes = NULL, Delta, 
                   Phi = NULL, S, Theta2, BatchInfo)

# Simulated parameter values for 10 genes
# (7 biogical and 3 spike-in) measured in 5 cells
Mu <- c(8.36, 10.65, 4.88, 6.29, 21.72, 12.93, 30.19)
Mu_spikes <-  c(1010.72, 7.90, 31.59)
Delta <- c(1.29, 0.88, 1.51, 1.49, 0.54, 0.40, 0.85)
Phi <- c(1.00, 1.06, 1.09, 1.05, 0.80)
S <- c(0.38, 0.40, 0.38, 0.39, 0.34)
Theta <- 0.39

# Data with spike-ins, single batch
Data <- BASiCS_Sim(Mu, Mu_spikes, Delta, Phi, S, Theta)
head(SingleCellExperiment::counts(Data))
dim(SingleCellExperiment::counts(Data))
altExp(Data)
rowData(altExp(Data))

# Data with spike-ins, multiple batches
BatchInfo <- c(1,1,1,2,2)
Theta2 <- rep(Theta, times = 2)
Data <- BASiCS_Sim(Mu, Mu_spikes, Delta, Phi, S, Theta2, BatchInfo)

# Data without spike-ins, multiple batches
Data <- BASiCS_Sim(Mu, Mu_spikes = NULL, Delta, 
                   Phi = NULL, S, Theta2, BatchInfo)

The BASiCS_Summary class

Description

Container of a summary of a BASiCS_Chain object. In each element of the parameters slot, first column contains posterior medians; second and third columns respectively contain the lower and upper limits of an high posterior density interval (for a given probability).

Slots

parameters

List of parameters in which each entry contains a matrix: first column contains posterior medians, second column contains the lower limits of an high posterior density interval and third column contains the upper limits of high posterior density intervals.

mu: Posterior medians (1st column), lower (2nd column) and upper (3rd column) limits of gene-specific mean expression parameters $\mu_i$ .
delta: Posterior medians (1st column), lower (2nd column) and upper (3rd column) limits of gene-specific biological over-dispersion parameters $\delta_i$ , biological genes only
phi: Posterior medians (1st column), lower (2nd column) and upper (3rd column) limits of cell-specific mRNA content normalisation parameters $\phi_j$
s: Posterior medians (1st column), lower (2nd column) and upper (3rd column) limits of cell-specific technical normalisation parameters $s[j]$
nu: Posterior medians (1st column), lower (2nd column) and upper (3rd column) limits of cell-specific random effects $\nu_j$
theta: Posterior median (1st column), lower (2nd column) and upper (3rd column) limits of technical over-dispersion parameter(s) $\theta$ (each row represents one batch)
beta: Posterior median (first column), lower (second column) and upper (third column) limits of regression coefficients $\beta$
sigma2: Posterior median (first column), lower (second column) and upper (third column) limits of residual variance $\sigma^2$
epsilon: Posterior median (first column), lower (second column) and upper (third column) limits of gene-specific residual over-dispersion parameter $\epsilon$

Examples


# A BASiCS_Summary object created by the Summary method.
Data <- makeExampleBASiCS_Data()
Chain <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2, Regression = FALSE)
ChainSummary <- Summary(Chain)


# A BASiCS_Summary object created by the Summary method.
Data <- makeExampleBASiCS_Data()
Chain <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2, Regression = FALSE)
ChainSummary <- Summary(Chain)

'show' method for BASiCS_Summary objects

Description

'show' method for BASiCS_Summary objects.

Usage

## S4 method for signature 'BASiCS_Summary'
show(object)
## S4 method for signature 'BASiCS_Summary'
show(object)

Arguments

object

A BASiCS_Summary object.

Value

Prints a summary of the properties of object.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


data(ChainSC)
show(ChainSC)

data(ChainSC)
show(ChainSC)

Detection of genes with changes in expression

Description

Function to assess changes in expression between two groups of cells (mean and over-dispersion)

Usage

BASiCS_TestDE(
  Chain1,
  Chain2,
  EpsilonM = log2(1.5),
  EpsilonD = log2(1.5),
  EpsilonR = log2(1.5)/log2(exp(1)),
  ProbThresholdM = 2/3,
  ProbThresholdD = 2/3,
  ProbThresholdR = 2/3,
  OrderVariable = c("GeneIndex", "GeneName", "Mu"),
  GroupLabel1 = "Group1",
  GroupLabel2 = "Group2",
  Plot = TRUE,
  PlotOffset = TRUE,
  PlotOffsetType = c("offset estimate", "before-after", "MA plot"),
  Offset = TRUE,
  EFDR_M = 0.05,
  EFDR_D = 0.05,
  EFDR_R = 0.05,
  GenesSelect = rep(TRUE, ncol(Chain1@parameters[["mu"]])),
  min.mean = 1,
  MinESS = 100,
  ...
)
BASiCS_TestDE(
  Chain1,
  Chain2,
  EpsilonM = log2(1.5),
  EpsilonD = log2(1.5),
  EpsilonR = log2(1.5)/log2(exp(1)),
  ProbThresholdM = 2/3,
  ProbThresholdD = 2/3,
  ProbThresholdR = 2/3,
  OrderVariable = c("GeneIndex", "GeneName", "Mu"),
  GroupLabel1 = "Group1",
  GroupLabel2 = "Group2",
  Plot = TRUE,
  PlotOffset = TRUE,
  PlotOffsetType = c("offset estimate", "before-after", "MA plot"),
  Offset = TRUE,
  EFDR_M = 0.05,
  EFDR_D = 0.05,
  EFDR_R = 0.05,
  GenesSelect = rep(TRUE, ncol(Chain1@parameters[["mu"]])),
  min.mean = 1,
  MinESS = 100,
  ...
)

Arguments

`Chain1`	an object of class `BASiCS_Chain` containing parameter estimates for the first group of cells
`Chain2`	an object of class `BASiCS_Chain` containing parameter estimates for the second group of cells
`EpsilonM`	Minimum fold change tolerance threshold for detecting changes in overall expression (must be a positive real number). Default value: `EpsilonM = log2(1.5)` (i.e. 50% increase).
`EpsilonD`	Minimum fold change tolerance threshold for detecting changes in biological over-dispersion (must be a positive real number). Default value: `EpsilonM = log2(1.5)` (i.e. 50% increase).
`EpsilonR`	Minimum distance threshold for detecting changes in residual over-dispersion (must be a positive real number). Default value: `EpsilonR= log2(1.5)/log2(exp(1))` (i.e. 50% increase).
`ProbThresholdM`	Optional parameter. Probability threshold for detecting changes in overall expression (must be a positive value, between 0 and 1). If `EFDR_M = NULL`, the posterior probability threshold for the differential mean expression test will be set to `ProbThresholdM`. If a value for `EFDR_M` is provided, the posterior probability threshold is chosen to achieve an EFDR equal to `EFDR_M` and `ProbThresholdM` defines a minimum probability threshold for this calibration (this avoids low values of `ProbThresholdM` to be chosen by the EFDR calibration. Default value `ProbThresholdM = 2/3`, i.e. the probability of observing a log2-FC above `EpsilonM` must be at least twice the probality of observing the complementary event (log2-FC below `EpsilonM`).
`ProbThresholdD`	Optional parameter. Probability threshold for detecting changes in cell-to-cell biological over-dispersion (must be a positive value, between 0 and 1). Same usage as `ProbThresholdM`, depending on the value provided for `EFDR_D`. Default value `ProbThresholdD = 2/3`.
`ProbThresholdR`	Optional parameter. Probability threshold for detecting changes in residual over-dispersion (must be a positive value, between 0 and 1). Same usage as `ProbThresholdM`, depending on the value provided for `EFDR_R`. Default value `ProbThresholdR = 2/3`.
`OrderVariable`	Ordering variable for output. Possible values: `'GeneIndex'` (default), `'GeneName'` and `'Mu'` (mean expression).
`GroupLabel1`	Label assigned to reference group. Default: `GroupLabel1 = 'Group1'`
`GroupLabel2`	Label assigned to reference group. Default: `GroupLabel2 = 'Group2'`
`Plot`	If `Plot = TRUE`, MA and volcano plots are generated.
`PlotOffset`	If `Plot = TRUE`, the offset effect is visualised.
`PlotOffsetType`	See argument `Type` in `BASiCS_PlotOffset` for more information.
`Offset`	Optional argument to remove a fix offset effect (if not previously removed from the MCMC chains). Default: `Offset = TRUE`.
`EFDR_M`	Target for expected false discovery rate related to the comparison of means. If `EFDR_M = NULL`, EFDR calibration is not performed and the posterior probability threshold is set equal to `ProbThresholdM`. Default `EFDR_M = 0.05`.
`EFDR_D`	Target for expected false discovery rate related to the comparison of dispersions. If `EFDR_D = NULL`, EFDR calibration is not performed and the posterior probability threshold is set equal to `ProbThresholdD`.Default `EFDR_D = 0.05`.
`EFDR_R`	Target for expected false discovery rate related to the comparison of residual over-dispersions. If `EFDR_R = NULL`, EFDR calibration is not performed and the posterior probability threshold is set equal to `ProbThresholdR`.Default `EFDR_D = 0.05`.
`GenesSelect`	Optional argument to provide a user-defined list of genes to be considered for the comparison. Default: `GenesSelect = rep(TRUE, nGene)` When used, this argument must be a vector of `TRUE` (include gene) / `FALSE` (exclude gene) indicator, with the same length as the number of intrinsic genes and following the same order as how genes are displayed in the table of counts. This argument is necessary in order to have a meaningful EFDR calibration when the user decides to exclude some genes from the comparison.
`min.mean`	Minimum mean expression threshold required for inclusion in offset calculation. Similar to 'min.mean' in 'scran::computeSumFactors'. This parameter is only relevant with 'Offset = TRUE'.
`MinESS`	The minimum effective sample size for a gene to be included in the tests for differential expression. This helps to remove genes with poor mixing from differential expression tests. Default is 100. If set to NA, genes are not checked for effective sample size before differential expression tests are performed.
`...`	Optional parameters.

Value

BASiCS_TestDE returns an object of class BASiCS_ResultsDE

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


# Loading two 'BASiCS_Chain' objects (obtained using 'BASiCS_MCMC')
data(ChainSC)
data(ChainRNA)

Test <- BASiCS_TestDE(
  Chain1 = ChainSC, Chain2 = ChainRNA,
  GroupLabel1 = "SC", GroupLabel2 = "P&S",
  EpsilonM = log2(1.5), EpsilonD = log2(1.5),
  OffSet = TRUE
)

# Results for the differential mean test
head(as.data.frame(Test, Parameter = "Mean"))

# Results for the differential over-dispersion test
# This only includes genes marked as 'NoDiff' in Test$TableMean
head(as.data.frame(Test, Parameter = "Disp"))

# For testing differences in residual over-dispersion, two chains obtained
# via 'BASiCS_MCMC(Data, N, Thin, Burn, Regression=TRUE)' need to be provided
data(ChainSCReg)
data(ChainRNAReg)

Test <- BASiCS_TestDE(
  Chain1 = ChainSCReg, Chain2 = ChainRNAReg,
  GroupLabel1 = 'SC', GroupLabel2 = 'P&S',
  EpsilonM = log2(1.5), EpsilonD = log2(1.5),
  EpsilonR = log2(1.5)/log2(exp(1)),
  OffSet = TRUE
)

## Plotting the results of these tests
BASiCS_PlotDE(Test)
# Loading two 'BASiCS_Chain' objects (obtained using 'BASiCS_MCMC')
data(ChainSC)
data(ChainRNA)

Test <- BASiCS_TestDE(
  Chain1 = ChainSC, Chain2 = ChainRNA,
  GroupLabel1 = "SC", GroupLabel2 = "P&S",
  EpsilonM = log2(1.5), EpsilonD = log2(1.5),
  OffSet = TRUE
)

# Results for the differential mean test
head(as.data.frame(Test, Parameter = "Mean"))

# Results for the differential over-dispersion test
# This only includes genes marked as 'NoDiff' in Test$TableMean
head(as.data.frame(Test, Parameter = "Disp"))

# For testing differences in residual over-dispersion, two chains obtained
# via 'BASiCS_MCMC(Data, N, Thin, Burn, Regression=TRUE)' need to be provided
data(ChainSCReg)
data(ChainRNAReg)

Test <- BASiCS_TestDE(
  Chain1 = ChainSCReg, Chain2 = ChainRNAReg,
  GroupLabel1 = 'SC', GroupLabel2 = 'P&S',
  EpsilonM = log2(1.5), EpsilonD = log2(1.5),
  EpsilonR = log2(1.5)/log2(exp(1)),
  OffSet = TRUE
)

## Plotting the results of these tests
BASiCS_PlotDE(Test)

Decomposition of gene expression variability according to BASiCS

Description

Function to decompose total variability of gene expression into biological and technical components.

Usage

BASiCS_VarianceDecomp(
  Chain,
  OrderVariable = c("BioVarGlobal", "GeneName", "TechVarGlobal", "ShotNoiseGlobal"),
  Plot = TRUE,
  main = "Overall variance decomposition",
  ylab = "% of variance",
  beside = FALSE,
  palette = "Set1",
  legend = c("Biological", "Technical", "Shot noise"),
  names.arg = if (nBatch == 1) "Overall" else c("Overall", paste("Batch",
    seq_len(nBatch)))
)
BASiCS_VarianceDecomp(
  Chain,
  OrderVariable = c("BioVarGlobal", "GeneName", "TechVarGlobal", "ShotNoiseGlobal"),
  Plot = TRUE,
  main = "Overall variance decomposition",
  ylab = "% of variance",
  beside = FALSE,
  palette = "Set1",
  legend = c("Biological", "Technical", "Shot noise"),
  names.arg = if (nBatch == 1) "Overall" else c("Overall", paste("Batch",
    seq_len(nBatch)))
)

Arguments

`Chain`	an object of class `BASiCS_Chain`
`OrderVariable`	Ordering variable for output. Possible values: `'GeneName'`, `'BioVarGlobal'`, `'TechVarGlobal'` and `'ShotNoiseGlobal'`. Default: `OrderVariable = "BioVarGlobal"`.
`Plot`	If `TRUE`, a barplot of the variance decomposition (global and by batches, if any) is generated. Default: `Plot = TRUE`.
`main`	Plot title.
`ylab`	y axis label.
`beside`	If `TRUE`, bars are placed beside each other. If `FALSE`, bars are stacked.
`palette`	Palette to be passed to `scale_fill_brewer` to create a discrete colour mapping.
`legend`	Labels for variance components.
`names.arg`	X axis labels.

Details

See vignette

Value

A data.frame whose first 4 columns correspond to

GeneName: Gene name (as indicated by user)
BioVarGlobal: Percentage of variance explained by a biological component (overall across all cells)
TechVarGlobal: Percentage of variance explained by the technical component (overall across all cells)
ShotNoiseGlobal: Percentage of variance explained by the shot noise component (baseline Poisson noise, overall across all cells)

If more than 1 batch of cells are being analysed, the remaining columns contain the corresponding variance decomposition calculated within each batch.

Author(s)

Catalina A. Vallejos [email protected]

References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

Examples


# For illustration purposes we load a built-in 'BASiCS_Chain' object
# (obtained using the 'BASiCS_MCMC' function)
data(ChainSC)

VD <- BASiCS_VarianceDecomp(ChainSC)

# For illustration purposes we load a built-in 'BASiCS_Chain' object
# (obtained using the 'BASiCS_MCMC' function)
data(ChainSC)

VD <- BASiCS_VarianceDecomp(ChainSC)

Detection method for highly and lowly variable genes using a grid of variance contribution thresholds

Description

Detection method for highly and lowly variable genes using a grid of variance contribution thresholds. Only used when HVG/LVG are found based on the variance decomposition.

Usage

BASiCS_VarThresholdSearchVG(
  Chain,
  Task = c("HVG", "LVG"),
  VarThresholdsGrid,
  EFDR = 0.1,
  Progress = TRUE
)

BASiCS_VarThresholdSearchHVG(...)

BASiCS_VarThresholdSearchLVG(...)
BASiCS_VarThresholdSearchVG(
  Chain,
  Task = c("HVG", "LVG"),
  VarThresholdsGrid,
  EFDR = 0.1,
  Progress = TRUE
)

BASiCS_VarThresholdSearchHVG(...)

BASiCS_VarThresholdSearchLVG(...)

Arguments

`Chain`	an object of class `BASiCS_Chain`
`Task`	See `?BASiCS_DetectVG`.
`VarThresholdsGrid`	Grid of values for the variance contribution threshold (they must be contained in (0,1))
`EFDR`	Target for expected false discovery rate related to HVG/LVG detection. Default: `EFDR = 0.10`.
`Progress`	If `Progress = TRUE`, partial output is printed in the console. Default: `Progress = TRUE`.
`...`	Passed to methods.

Details

See vignette

Value

BASiCS_VarThresholdSearchHVG: A table displaying the results of highly variable genes detection for different variance contribution thresholds.
BASiCS_VarThresholdSearchLVG: A table displaying the results of lowly variable genes detection for different variance contribution thresholds.

Author(s)

Catalina A. Vallejos [email protected]

References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

Examples


data(ChainSC)

BASiCS_VarThresholdSearchHVG(ChainSC,
                             VarThresholdsGrid = seq(0.55,0.65,by=0.01),
                             EFDR = 0.10)
BASiCS_VarThresholdSearchLVG(ChainSC,
                             VarThresholdsGrid = seq(0.35,0.45,by=0.01),
                             EFDR = 0.10)

data(ChainSC)

BASiCS_VarThresholdSearchHVG(ChainSC,
                             VarThresholdsGrid = seq(0.55,0.65,by=0.01),
                             EFDR = 0.10)
BASiCS_VarThresholdSearchLVG(ChainSC,
                             VarThresholdsGrid = seq(0.35,0.45,by=0.01),
                             EFDR = 0.10)

Defunct functions in package ‘BASiCS’

Description

The functions listed here are no longer part of BASiCS.

Details

## Removed

BASiCS_D_TestDE has been replaced by BASiCS_TestDE.

usage

## Removed

BASiCS_D_TestDE()

Author(s)

Catalina A. Vallejos [email protected]

Extract from the chain obtained for the Grun et al (2014) data: pool-and-split samples

Description

Small extract (75 MCMC iterations, 350 randomly selected genes) from the chain obtained for the pool-and-split samples (this corresponds to the RNA 2i samples in Grun et al, 2014).

Usage

ChainRNA
ChainRNA

Format

An object of class BASiCS_Chain containing 75 MCMC iterations.

References

Grun, Kester and van Oudenaarden (2014). Nature Methods.

Extract from the chain obtained for the Grun et al (2014) data: pool-and-split samples (regression model)

Description

Small extract (75 MCMC iterations, 350 randomly selected genes) from the chain obtained for the pool-and-split samples (this corresponds to the RNA 2i samples in Grun et al, 2014).

Usage

ChainRNAReg
ChainRNAReg

Format

An object of class BASiCS_Chain containing 75 MCMC iterations.

References

Grun, Kester and van Oudenaarden (2014). Nature Methods.

Extract from the chain obtained for the Grun et al (2014) data: single-cell samples

Description

Small extract (75 MCMC iterations, 350 randomly selected genes) from the chain obtained for the pool-and-split samples (this corresponds to the SC 2i samples in Grun et al, 2014).

Usage

ChainSC
ChainSC

Format

An object of class BASiCS_Chain containing 75 MCMC iterations.

References

Grun, Kester and van Oudenaarden (2014). Nature Methods.

Extract from the chain obtained for the Grun et al (2014) data: single-cell samples (regression model)

Description

Small extract (75 MCMC iterations, 350 randomly selected genes) from the chain obtained for the pool-and-split samples (this corresponds to the SC 2i samples in Grun et al, 2014).

Usage

ChainSCReg
ChainSCReg

Format

An object of class BASiCS_Chain containing 75 MCMC iterations.

References

Grun, Kester and van Oudenaarden (2014). Nature Methods.

'dim' method for BASiCS_Chain objects

Description

Returns the dimensions (genes x cells) of a BASiCS_Chain

Usage

## S4 method for signature 'BASiCS_Chain'
dim(x)
## S4 method for signature 'BASiCS_Chain'
dim(x)

Arguments

`x`	A `BASiCS_Chain` object.

Value

An vector of dimensions

Author(s)

Catalina A. Vallejos [email protected]

Examples


data(ChainSC)
dimnames(ChainSC)

data(ChainSC)
dimnames(ChainSC)

'dimnames' method for BASiCS_Chain objects

Description

Returns the dimension names (genes x cells) of a BASiCS_Chain

Usage

## S4 method for signature 'BASiCS_Chain'
dimnames(x)
## S4 method for signature 'BASiCS_Chain'
dimnames(x)

Arguments

`x`	A `BASiCS_Chain` object.

Value

A list of two elements: (1) a vector of gene names and (2) a vector of cell names.

Author(s)

Catalina A. Vallejos [email protected]

Examples


data(ChainSC)
dimnames(ChainSC)

data(ChainSC)
dimnames(ChainSC)

Accessors for the slots of a BASiCS_Chain object

Description

Accessors for the slots of a BASiCS_Chain

Usage

## S4 method for signature 'BASiCS_Chain'
displayChainBASiCS(object, Parameter = "mu")
## S4 method for signature 'BASiCS_Chain'
displayChainBASiCS(object, Parameter = "mu")

Arguments

`object`	an object of class `BASiCS_Chain`
`Parameter`	Name of the slot to be used for the accessed. Possible values: `'mu'`, `'delta'`, `'phi'`, `'s'`, `'nu'`, `'theta'`, `'beta'`, `'sigma2'` and `'epsilon'`.

Value

The requested slot of a BASiCS_Chain object

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


help(BASiCS_MCMC)

help(BASiCS_MCMC)

Accessors for the slots of a `BASiCS_Summary` object

Description

Accessors for the slots of a BASiCS_Summary object

Usage

## S4 method for signature 'BASiCS_Summary'
displaySummaryBASiCS(object, Parameter = "mu")
## S4 method for signature 'BASiCS_Summary'
displaySummaryBASiCS(object, Parameter = "mu")

Arguments

`object`	an object of class `BASiCS_Summary`
`Parameter`	Name of the slot to be used for the accessed. Possible values: `'mu'`, `'delta'`, `'phi'`, `'s'`, `'nu'`, `'theta'`, `'beta'`, `'sigma2'` and `'epsilon'`.

Value

The requested slot of a BASiCS_Summary object

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


help(BASiCS_MCMC)

help(BASiCS_MCMC)

Methods for formatting BASiCS_Result and BASiCS_ResultsDE objects.

Description

Methods for formatting BASiCS_Result and BASiCS_ResultsDE objects.

Usage

## S4 method for signature 'BASiCS_ResultsDE'
format(x, Parameter, Filter = TRUE, ProbThreshold = NULL, ...)

## S4 method for signature 'BASiCS_ResultDE'
format(x, Filter = TRUE, ProbThreshold = NULL, ...)

## S4 method for signature 'BASiCS_ResultVG'
format(x, Filter = TRUE, ProbThreshold = NULL, ...)
## S4 method for signature 'BASiCS_ResultsDE'
format(x, Parameter, Filter = TRUE, ProbThreshold = NULL, ...)

## S4 method for signature 'BASiCS_ResultDE'
format(x, Filter = TRUE, ProbThreshold = NULL, ...)

## S4 method for signature 'BASiCS_ResultVG'
format(x, Filter = TRUE, ProbThreshold = NULL, ...)

Arguments

`x`	Object being subsetted.
`Parameter`	Character scalar indicating which of the BASiCS_Result should be formatted.
`Filter`	Logical scalar indicating whether results should be filtered based on differential expression or HVG/LVG status if `ProbThreshold=NULL`, or a probability threshold if `ProbThreshold=NULL`
`ProbThreshold`	Probability threshold to be used if `Filter=TRUE`
`...`	Passed to `format`.

Value

A data.frame.

Create a synthetic SingleCellExperiment example object with the format required for BASiCS

Description

A synthetic SingleCellExperiment object is generated by simulating a dataset from the model underlying BASiCS. This is used to illustrate BASiCS in some of the package and vignette examples.

Usage

makeExampleBASiCS_Data(WithBatch = FALSE, WithSpikes = TRUE)
makeExampleBASiCS_Data(WithBatch = FALSE, WithSpikes = TRUE)

Arguments

`WithBatch`	If `TRUE`, 2 batches are generated (each of them containing 15 cells). Default: `WithBatch = FALSE`.
`WithSpikes`	If `TRUE`, the simulated dataset contains 20 spike-in genes. If `WithSpikes = FALSE`, `WithBatch` is automatically set to `TRUE`. Default: `WithSpikes = TRUE`

Details

Note: In BASiCS versions < 1.5.22, makeExampleBASiCS_Data used a fixed seed within the function. This has been removed to comply with Bioconductor policies. If a reproducible example is required, please use set.seed prior to calling makeExampleBASiCS_Data .

Value

An object of class SingleCellExperiment, with synthetic data simulated from the model implemented in BASiCS. If WithSpikes = TRUE, it contains 70 genes (50 biological and 20 spike-in) and 30 cells. Alternatively, it contains 50 biological genes and 30 cells.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples

Data <- makeExampleBASiCS_Data()
is(Data, 'SingleCellExperiment')

Data <- makeExampleBASiCS_Data()
is(Data, 'SingleCellExperiment')

Creates a BASiCS_Chain object from pre-computed MCMC chains

Description

BASiCS_Chain creates a BASiCS_Chain object from pre-computed MCMC chains.

Usage

newBASiCS_Chain(parameters)
newBASiCS_Chain(parameters)

Arguments

parameters

List of matrices containing MCMC chains for each model parameter.

mu: MCMC chain for gene-specific mean expression parameters $\mu_i$ , biological genes only (matrix with q.bio columns, all elements must be positive numbers)
delta: MCMC chain for gene-specific biological over-dispersion parameters $\delta_i$ , biological genes only (matrix with q.bio columns, all elements must be positive numbers)
phi: MCMC chain for cell-specific mRNA content normalisation parameters $\phi_j$ (matrix with n columns, all elements must be positive numbers and the sum of its elements must be equal to n)

. This parameter is only used when spike-in genes are available.

s: MCMC chain for cell-specific technical normalisation parameters $s_j$ (matrix with n columns, all elements must be positive numbers)
nu: MCMC chain for cell-specific random effects $\nu_j$ (matrix with n columns, all elements must be positive numbers)
theta: MCMC chain for technical over-dispersion parameter(s) $\theta$ (matrix, all elements must be positive, each colum represents 1 batch)
beta: Only used for regression model. MCMC chain for regression coefficients (matrix with k columns, where k represent the number of chosen basis functions + 2)
sigma2: Only used for regression model. MCMC chain for the residual variance (matrix with one column, sigma2 represents a global parameter)
epsilon: Only used for regression model. MCMC chain for the gene specific residual over-dispersion parameter (mean corrected vraribility) (matrix with q columns)

Value

An object of class BASiCS_Chain.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


Data <- makeExampleBASiCS_Data()

# No regression model
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 5, Burn = 5, Regression = FALSE)

ChainMu <- displayChainBASiCS(Chain, 'mu')
ChainDelta <- displayChainBASiCS(Chain, 'delta')
ChainPhi <- displayChainBASiCS(Chain, 'phi')
ChainS <- displayChainBASiCS(Chain, 's')
ChainNu <- displayChainBASiCS(Chain, 'nu')
ChainTheta <- displayChainBASiCS(Chain, 'theta')

ChainNew <- newBASiCS_Chain(parameters = list(mu = ChainMu, 
                                              delta = ChainDelta,
                                              phi = ChainPhi, 
                                              s = ChainS, 
                                              nu = ChainNu, 
                                              theta = ChainTheta))
                            

# No regression model
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 5, Burn = 5, Regression = TRUE)

ChainMu <- displayChainBASiCS(Chain, 'mu')
ChainDelta <- displayChainBASiCS(Chain, 'delta')
ChainPhi <- displayChainBASiCS(Chain, 'phi')
ChainS <- displayChainBASiCS(Chain, 's')
ChainNu <- displayChainBASiCS(Chain, 'nu')
ChainTheta <- displayChainBASiCS(Chain, 'theta')
ChainBeta <- displayChainBASiCS(Chain, 'beta')
ChainSigma2 <- displayChainBASiCS(Chain, 'sigma2')
ChainEpsilon <- displayChainBASiCS(Chain, 'epsilon')

ChainNew <- newBASiCS_Chain(parameters = list(mu = ChainMu, 
                                              delta = ChainDelta,
                                              phi = ChainPhi, 
                                              s = ChainS, 
                                              nu = ChainNu, 
                                              theta = ChainTheta,
                                              beta = ChainBeta, 
                                              sigma2 = ChainSigma2,
                                              epsilon = ChainEpsilon))

Data <- makeExampleBASiCS_Data()

# No regression model
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 5, Burn = 5, Regression = FALSE)

ChainMu <- displayChainBASiCS(Chain, 'mu')
ChainDelta <- displayChainBASiCS(Chain, 'delta')
ChainPhi <- displayChainBASiCS(Chain, 'phi')
ChainS <- displayChainBASiCS(Chain, 's')
ChainNu <- displayChainBASiCS(Chain, 'nu')
ChainTheta <- displayChainBASiCS(Chain, 'theta')

ChainNew <- newBASiCS_Chain(parameters = list(mu = ChainMu, 
                                              delta = ChainDelta,
                                              phi = ChainPhi, 
                                              s = ChainS, 
                                              nu = ChainNu, 
                                              theta = ChainTheta))
                            

# No regression model
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 5, Burn = 5, Regression = TRUE)

ChainMu <- displayChainBASiCS(Chain, 'mu')
ChainDelta <- displayChainBASiCS(Chain, 'delta')
ChainPhi <- displayChainBASiCS(Chain, 'phi')
ChainS <- displayChainBASiCS(Chain, 's')
ChainNu <- displayChainBASiCS(Chain, 'nu')
ChainTheta <- displayChainBASiCS(Chain, 'theta')
ChainBeta <- displayChainBASiCS(Chain, 'beta')
ChainSigma2 <- displayChainBASiCS(Chain, 'sigma2')
ChainEpsilon <- displayChainBASiCS(Chain, 'epsilon')

ChainNew <- newBASiCS_Chain(parameters = list(mu = ChainMu, 
                                              delta = ChainDelta,
                                              phi = ChainPhi, 
                                              s = ChainS, 
                                              nu = ChainNu, 
                                              theta = ChainTheta,
                                              beta = ChainBeta, 
                                              sigma2 = ChainSigma2,
                                              epsilon = ChainEpsilon))

Creates a SingleCellExperiment object from a matrix of expression counts and experimental information about spike-in genes

Description

newBASiCS_Data creates a SingleCellExperiment object from a matrix of expression counts and experimental information about spike-in genes.

Usage

newBASiCS_Data(
  Counts,
  Tech = rep(FALSE, nrow(Counts)),
  SpikeInfo = NULL,
  BatchInfo = NULL,
  SpikeType = "ERCC"
)
newBASiCS_Data(
  Counts,
  Tech = rep(FALSE, nrow(Counts)),
  SpikeInfo = NULL,
  BatchInfo = NULL,
  SpikeType = "ERCC"
)

Arguments

`Counts`	Matrix of dimensions `q` times `n` whose elements contain the expression counts to be analyses (including biological and technical spike-in genes). Gene names must be stored as `rownames(Counts)`.
`Tech`	Logical vector of length `q`. If `Tech = FALSE` the gene is biological; otherwise the gene is spike-in. Defaul value: `Tech = rep(FALSE, nrow(Counts))`.
`SpikeInfo`	`data.frame` whose first and second columns contain the gene names assigned to the spike-in genes (they must match the ones in `rownames(Counts)`) and the associated input number of molecules, respectively. If `SpikeInfo = NULL`, only the horizontal integration implementation (no spikes) can be run. Default value: `SpikeInfo = NULL`.
`BatchInfo`	Vector of length `n` whose elements indicate batch information. Not required if a single batch is present on the data. Default value: `BatchInfo = NULL`.
`SpikeType`	Character to indicate what type of spike-ins are in use. Default value: `SpikeType = "ERCC"` (parameter is no longer used).

Value

An object of class SingleCellExperiment.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

'plot' method for BASiCS_Chain objects

Description

'plot' method for BASiCS_Chain objects

Usage

## S4 method for signature 'BASiCS_Chain,ANY'
plot(
  x,
  Parameter = "mu",
  Gene = NULL,
  Cell = NULL,
  Batch = 1,
  RegressionTerm = NULL,
  ...
)
## S4 method for signature 'BASiCS_Chain,ANY'
plot(
  x,
  Parameter = "mu",
  Gene = NULL,
  Cell = NULL,
  Batch = 1,
  RegressionTerm = NULL,
  ...
)

Arguments

`x`	A `BASiCS_Chain` object.
`Parameter`	Name of the slot to be used for the plot. Possible values: `'mu'`, `'delta'`, `'phi'`, `'s'`, `'nu'`, `'theta'`, `'beta'`, `'sigma2'` and `'epsilon'`.
`Gene`	Specifies which gene is requested. Required only if `Parameter = 'mu'` or `'delta'`
`Cell`	Specifies which cell is requested. Required only if `Parameter = 'phi', 's'` or `'nu'`
`Batch`	Specifies which batch is requested. Required only if `Parameter = 'theta'`
`RegressionTerm`	Specifies which regression coefficient is requested. Required only if `Parameter = 'beta'`
`...`	Unused.

Value

A plot object

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


help(BASiCS_MCMC)

help(BASiCS_MCMC)

'plot' method for BASiCS_Summary objects

Description

'plot' method for BASiCS_Summary objects

Usage

## S4 method for signature 'BASiCS_Summary,ANY'
plot(
  x,
  Param = "mu",
  Param2 = NULL,
  Genes = NULL,
  Cells = NULL,
  Batches = NULL,
  RegressionTerms = NULL,
  xlab = "",
  ylab = "",
  xlim = "",
  ylim = NULL,
  pch = 16,
  col = "blue",
  bty = "n",
  SmoothPlot = TRUE,
  ...
)
## S4 method for signature 'BASiCS_Summary,ANY'
plot(
  x,
  Param = "mu",
  Param2 = NULL,
  Genes = NULL,
  Cells = NULL,
  Batches = NULL,
  RegressionTerms = NULL,
  xlab = "",
  ylab = "",
  xlim = "",
  ylim = NULL,
  pch = 16,
  col = "blue",
  bty = "n",
  SmoothPlot = TRUE,
  ...
)

Arguments

`x`	A `BASiCS_Summary` object.
`Param`	Name of the slot to be used for the plot. Possible values: `'mu'`, `'delta'`, `'phi'`, `'s'`, `'nu'`, `'theta'`, `'beta'`, `'sigma2'` and `'epsilon'`.
`Param2`	Name of the second slot to be used for the plot. Possible values: `'mu'`, `'delta'`, `'epsilon'`, `'phi'`, `'s'` and `'nu'` (combinations between gene-specific and cell-specific parameters are not admitted).
`Genes`	Specifies which genes are requested. Required only if `Param = 'mu'`, `'delta'` or `'epsilon'`.
`Cells`	Specifies which cells are requested. Required only if `Param = 'phi', 's'` or `'nu'`
`Batches`	Specifies which batches are requested. Required only if `Param = 'theta'`
`RegressionTerms`	Specifies which regression coefficients are requested. Required only if `Param = 'beta'`
`xlab`	As in `par`.
`ylab`	As in `par`.
`xlim`	As in `par`.
`ylim`	As in `par`.
`pch`	As in `par`.
`col`	As in `par`.
`bty`	As in `par`.
`SmoothPlot`	Logical parameter. If `TRUE`, transparency will be added to the color of the dots.
`...`	Other graphical parameters (see `par`).

Value

A plot object

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


help(BASiCS_MCMC)

help(BASiCS_MCMC)

rowData getter and setter for BASiCS_ResultsDE and BASiCS_ResultVG objects.

Description

rowData getter and setter for BASiCS_ResultsDE and BASiCS_ResultVG objects.

Usage

## S4 method for signature 'BASiCS_ResultsDE'
rowData(x)

## S4 replacement method for signature 'BASiCS_ResultsDE'
rowData(x) <- value

## S4 method for signature 'BASiCS_ResultVG'
rowData(x)

## S4 replacement method for signature 'BASiCS_ResultVG'
rowData(x) <- value
## S4 method for signature 'BASiCS_ResultsDE'
rowData(x)

## S4 replacement method for signature 'BASiCS_ResultsDE'
rowData(x) <- value

## S4 method for signature 'BASiCS_ResultVG'
rowData(x)

## S4 replacement method for signature 'BASiCS_ResultVG'
rowData(x) <- value

Arguments

`x`	BASiCS_ResultVG or BASiCS_ResultsDE object.
`value`	New `rowData` value for setter method.

Value

For the getter, a DFrame. For setter, the modified x.

Accessors for the slots of a `BASiCS_ResultDE` object

Description

Accessors for the slots of a BASiCS_ResultDE object

Usage

## S4 method for signature 'BASiCS_ResultDE'
show(object)
## S4 method for signature 'BASiCS_ResultDE'
show(object)

Arguments

object

an object of class BASiCS_ResultDE

Value

Prints a summary of the properties of object.

Examples


help(BASiCS_MCMC)

help(BASiCS_MCMC)

Accessors for the slots of a `BASiCS_ResultsDE` object

Description

Accessors for the slots of a BASiCS_ResultsDE object

Usage

## S4 method for signature 'BASiCS_ResultsDE'
show(object)
## S4 method for signature 'BASiCS_ResultsDE'
show(object)

Arguments

object

an object of class BASiCS_ResultsDE

Value

Prints a summary of the properties of object.

Examples


help(BASiCS_MCMC)

help(BASiCS_MCMC)

Accessors for the slots of a `BASiCS_ResultVG` object

Description

Accessors for the slots of a BASiCS_ResultVG object

Usage

## S4 method for signature 'BASiCS_ResultVG'
show(object)
## S4 method for signature 'BASiCS_ResultVG'
show(object)

Arguments

object

an object of class BASiCS_ResultsDE

Value

Prints a summary of the properties of object.

Examples


help(BASiCS_MCMC)

help(BASiCS_MCMC)

A 'subset' method for 'BASiCS_Chain“ objects

Description

This can be used to extract a subset of a 'BASiCS_Chain' object. The subset can contain specific genes, cells or MCMC iterations

Usage

## S4 method for signature 'BASiCS_Chain'
subset(x, Genes = NULL, Cells = NULL, Iterations = NULL)
## S4 method for signature 'BASiCS_Chain'
subset(x, Genes = NULL, Cells = NULL, Iterations = NULL)

Arguments

`x`	A `BASiCS_Chain` object.
`Genes`, `Cells`	A vector of characters, logical values, or numbers, indicating which cells or genes will be extracted.
`Iterations`	Numeric vector of positive integers indicating which MCMC iterations will be extracted. The maximum value in `Iterations` must be less or equal than the total number of iterations contained in the original `BASiCS_Chain` object.

Value

An object of class BASiCS_Chain.

Author(s)

Catalina A. Vallejos [email protected]

Examples


data(ChainSC)

# Extracts 3 first genes
ChainSC1 <- subset(ChainSC, Genes = rownames(ChainSC)[1:3])
# Extracts 3 first cells
ChainSC2 <- subset(ChainSC, Cells = colnames(ChainSC)[1:3])
# Extracts 10 first iterations
ChainSC3 <- subset(ChainSC, Iterations = 1:10)

data(ChainSC)

# Extracts 3 first genes
ChainSC1 <- subset(ChainSC, Genes = rownames(ChainSC)[1:3])
# Extracts 3 first cells
ChainSC2 <- subset(ChainSC, Cells = colnames(ChainSC)[1:3])
# Extracts 10 first iterations
ChainSC3 <- subset(ChainSC, Iterations = 1:10)

'Summary' method for BASiCS_Chain objects

Description

For each of the BASiCS parameters (see Vallejos et al 2015), Summary returns the corresponding postior medians and limits of the high posterior density interval (probabilty equal to prob)

Usage

## S4 method for signature 'BASiCS_Chain'
Summary(x, ..., prob = 0.95, na.rm = FALSE)
## S4 method for signature 'BASiCS_Chain'
Summary(x, ..., prob = 0.95, na.rm = FALSE)

Arguments

`x`	A `BASiCS_Chain` object.
`...`	Unused, only included for consistency with the generic.
`prob`	`prob` argument for `HPDinterval` function.
`na.rm`	Unused, only included for consistency with the generic.

Value

An object of class BASiCS_Summary.

Author(s)

Catalina A. Vallejos [email protected]

Nils Eling [email protected]

Examples


data(ChainSC)
SummarySC <- Summary(ChainSC)

data(ChainSC)
SummarySC <- Summary(ChainSC)

Package 'BASiCS'

Help Index

Generate balanced subsets for divide and conquer BASiCS

Description

Usage

Arguments

Value

Methods for subsetting BASiCS_Result and BASiCS_ResultsDE objects.

Description

Usage

Arguments

Value

Converting BASiCS results objects to data.frames

Description

Usage

Arguments

Value

Convert concentration in moles per microlitre to molecule counts

Description

Usage

Arguments

Value

The BASiCS_Chain class

Description

Slots

Author(s)

Examples

'show' method for BASiCS_Chain objects

Description

Usage

Arguments

Value

Author(s)

Examples

Remove global mean expression offset

Description

Usage

Arguments

Value

Author(s)

Examples

Calculates denoised expression expression counts

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Calculates denoised expression rates

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Detection method for highly (HVG) and lowly (LVG) variable genes

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Examples

Create diagnostic plots of MCMC parameters

Description

Usage

Arguments

Value

Author(s)

References

See Also

Examples

Create diagnostic plots of MCMC parameters

Description

Loads pre-computed MCMC chains generated by the `BASiCS_MCMC` function