Package 'DMCFB' reference manual

Title:	Differentially Methylated Cytosines via a Bayesian Functional Approach
Description:	DMCFB is a pipeline for identifying differentially methylated cytosines using a Bayesian functional regression model in bisulfite sequencing data. By using a functional regression data model, it tries to capture position-specific, group-specific and other covariates-specific methylation patterns as well as spatial correlation patterns and unknown underlying models of methylation data. It is robust and flexible with respect to the true underlying models and inclusion of any covariates, and the missing values are imputed using spatial correlation between positions and samples. A Bayesian approach is adopted for estimation and inference in the proposed method.
Authors:	Farhad Shokoohi [aut, cre]
Maintainer:	Farhad Shokoohi <[email protected]>
License:	GPL-3
Version:	1.19.0
Built:	2024-06-30 06:15:11 UTC
Source:	https://github.com/bioc/DMCFB

Differentially Methylated cytosines using functional Bayesian regression models

Description

DMCFB is a profiling tool for identifying differentially methylated cytosines using Functional Bayesian Model in bisulfite sequencing data.

`DMCFB` methods

findDMCFB, plotDMCFB, cBSDMC, readBismark.

`BSDMC` objects

BSDMC-class

BSDMC object

Description

The BSDMC object is an S4 class that represents differentially methylated CpG sites (DMCs) in BS-Seq Data.

Arguments

`methReads`	The matrix `methReads` contains the number of methylated reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`totalReads`	The matrix `totalReads` contains the number of reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`methLevels`	The matrix `methLevels` contains the predicted methylation level spanning a CpG-site using Bayesian functional regression models. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.

Value

A BSDMC-class object

Slots

methReads: An integer matrix
totalReads: An integer matrix
methLevels: A numeric matrix

Author(s)

Farhad Shokoohi <[email protected]>

Examples

nr <- 500
nc <- 16
metht <- matrix(as.integer(runif(nr * nc, 0, nr)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
meths <- matrix(as.integer(runif(nr * nc, 0, 10)), nr)
methl <- methc / metht
methv <- matrix((runif(nr * nc, 0.1, 0.5)), nr)
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc])
OBJ2 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, methStates = meths, methVars = methv, colData = cd1
)
OBJ2
nr <- 500
nc <- 16
metht <- matrix(as.integer(runif(nr * nc, 0, nr)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
meths <- matrix(as.integer(runif(nr * nc, 0, 10)), nr)
methl <- methc / metht
methv <- matrix((runif(nr * nc, 0.1, 0.5)), nr)
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc])
OBJ2 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, methStates = meths, methVars = methv, colData = cd1
)
OBJ2

cBSDMC method

Description

Creates a BSDMC-class object

Usage

cBSDMC(
  methReads,
  totalReads,
  methLevels,
  rowRanges,
  colData = DataFrame(row.names = colnames(methReads)),
  metadata = list(),
  ...
)

## S4 method for signature 'matrix,matrix,matrix,GRanges'
cBSDMC(
  methReads,
  totalReads,
  methLevels,
  rowRanges,
  colData = DataFrame(row.names = colnames(methReads)),
  metadata = list(),
  ...
)
cBSDMC(
  methReads,
  totalReads,
  methLevels,
  rowRanges,
  colData = DataFrame(row.names = colnames(methReads)),
  metadata = list(),
  ...
)

## S4 method for signature 'matrix,matrix,matrix,GRanges'
cBSDMC(
  methReads,
  totalReads,
  methLevels,
  rowRanges,
  colData = DataFrame(row.names = colnames(methReads)),
  metadata = list(),
  ...
)

Arguments

`methReads`	The matrix `methReads` contains the number of methylated reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`totalReads`	The matrix `totalReads` contains the number of reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`methLevels`	The matrix `methLevels` contains the predicted methylation level spanning a CpG-site using Bayesian functional regression models. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`rowRanges`	A `GRanges` or `GRangesList` object describing the ranges of interest. Names, if present, become the row names of the `SummarizedExperiment` object. The length of the `GRanges` or `GRangesList` must equal the number of rows of the matrices in `assays`. If `rowRanges` is missing, a `SummarizedExperiment` instance is returned.
`colData`	Object of class `'DataFrame'` containing information on variable values of the samples
`metadata`	A `list` of storing MCMC samples or DMCs
`...`	other possible parameters

Details

The rows of a BSDMC object represent ranges (in genomic coordinates) of interest. The ranges of interest are described by a GRanges or a GRangesList object, accessible using the rowRanges function. The GRanges and GRangesList classes contains sequence (e.g., chromosome) name, genomic coordinates, and strand information. Each range can be annotated with additional data; this data might be used to describe the range or to summarize results (e.g., statistics of differential abundance) relevant to the range. Rows may or may not have row names; they often will not.

Value

A BSDMC-class

Author(s)

Farhad Shokoohi <[email protected]>

Examples

set.seed(1980)
nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
meths <- matrix(as.integer(runif(nr * nc, 0, 10)), nr)
methl <- methc / metht
methv <- matrix((runif(nr * nc, 0.1, 0.5)), nr)
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ2 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, methStates = meths, methVars = methv, colData = cd1
)
OBJ2
set.seed(1980)
nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
meths <- matrix(as.integer(runif(nr * nc, 0, 10)), nr)
methl <- methc / metht
methv <- matrix((runif(nr * nc, 0.1, 0.5)), nr)
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ2 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, methStates = meths, methVars = methv, colData = cd1
)
OBJ2

combine method

Description

combine two BSDMC-class or two BSDMC-class

Usage

combine(obj1, obj2)

## S4 method for signature 'BSDMC,BSDMC'
combine(obj1, obj2)
combine(obj1, obj2)

## S4 method for signature 'BSDMC,BSDMC'
combine(obj1, obj2)

Arguments

`obj1`	A `BSDMC-class`
`obj2`	A `BSDMC-class`

Value

A BSDMC-class or BSDMC-class

Author(s)

Farhad Shokoohi <[email protected]>

Examples

set.seed(1980)
nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc * 2, 0, nr)), nr)
methc <- matrix(
  rbinom(n = nr * nc, c(metht), prob = runif(nr * nc * 2)),
  nr, nc * 2
)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(Group = rep("G1", each = nc), row.names = LETTERS[1:nc])
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc[, 1:nc], totalReads = metht[, 1:nc],
  methLevels = methl[, 1:nc], colData = cd1
)
cd2 <- DataFrame(
  Group = rep("G2", each = nc),
  row.names = LETTERS[nc + 1:nc]
)
OBJ2 <- cBSDMC(
  rowRanges = r1, methReads = methc[, nc + 1:nc], totalReads =
    metht[, nc + 1:nc], methLevels = methl[, nc + 1:nc], colData = cd2
)
OBJ3 <- combine(OBJ1, OBJ2)
OBJ3
set.seed(1980)
nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc * 2, 0, nr)), nr)
methc <- matrix(
  rbinom(n = nr * nc, c(metht), prob = runif(nr * nc * 2)),
  nr, nc * 2
)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(Group = rep("G1", each = nc), row.names = LETTERS[1:nc])
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc[, 1:nc], totalReads = metht[, 1:nc],
  methLevels = methl[, 1:nc], colData = cd1
)
cd2 <- DataFrame(
  Group = rep("G2", each = nc),
  row.names = LETTERS[nc + 1:nc]
)
OBJ2 <- cBSDMC(
  rowRanges = r1, methReads = methc[, nc + 1:nc], totalReads =
    metht[, nc + 1:nc], methLevels = methl[, nc + 1:nc], colData = cd2
)
OBJ3 <- combine(OBJ1, OBJ2)
OBJ3

findDMCFB method

Description

DMC identification via Bayesian functional regression models

Usage

findDMCFB(
  object,
  bwa,
  bwb,
  nBurn,
  nMC,
  nThin,
  alpha,
  sdv,
  nCores,
  pSize,
  sfiles
)

## S4 method for signature 'BSDMC'
findDMCFB(
  object,
  bwa,
  bwb,
  nBurn,
  nMC,
  nThin,
  alpha,
  sdv,
  nCores,
  pSize,
  sfiles
)
findDMCFB(
  object,
  bwa,
  bwb,
  nBurn,
  nMC,
  nThin,
  alpha,
  sdv,
  nCores,
  pSize,
  sfiles
)

## S4 method for signature 'BSDMC'
findDMCFB(
  object,
  bwa,
  bwb,
  nBurn,
  nMC,
  nThin,
  alpha,
  sdv,
  nCores,
  pSize,
  sfiles
)

Arguments

`object`	A `BSDMC-class` object
`bwa`	An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the group-specific effects of the Bayesian functional regression model
`bwb`	An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the individual-specific effects of the Bayesian functional regression model
`nBurn`	An integer value specifying the number of burn-in samples
`nMC`	An integer value specifying the number of MCMC samples after burn-in
`nThin`	An integer value specifying the thining number in MCMC
`alpha`	A numeric value specifying the level of $\alpha$ in credible interval $(1-\alpha)\%$
`sdv`	An double value specifying the standard deviation of priors
`nCores`	An integer value specifying the number of machine cores for parallel computing
`pSize`	An integer value specifying the number of cytosines in a regrion to be used in a Bayesian functiona regression model for DMC detection
`sfiles`	A logical value indicating whether files to be saved or not.

Value

BSDMC-class object

Author(s)

Farhad Shokoohi <[email protected]>

Examples

set.seed(1980)
nr <- 1000
nc <- 4
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
OBJ2 <- findDMCFB(OBJ1,
  bwa = 10, bwb = 10, nBurn = 50, nMC = 50, nThin = 1,
  alpha = 0.05, nCores = 2, pSize = 500, sfiles = FALSE
)
OBJ2
set.seed(1980)
nr <- 1000
nc <- 4
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
OBJ2 <- findDMCFB(OBJ1,
  bwa = 10, bwb = 10, nBurn = 50, nMC = 50, nThin = 1,
  alpha = 0.05, nCores = 2, pSize = 500, sfiles = FALSE
)
OBJ2

methLevels method

Description

Returns methLevels stored in BSDMC-class

Assigns methLevels to BSDMC-class

Usage

methLevels(object)

methLevels(object) <- value

## S4 method for signature 'BSDMC'
methLevels(object)

## S4 replacement method for signature 'BSDMC,matrix'
methLevels(object) <- value
methLevels(object)

methLevels(object) <- value

## S4 method for signature 'BSDMC'
methLevels(object)

## S4 replacement method for signature 'BSDMC,matrix'
methLevels(object) <- value

Arguments

`object`	A `BSDMC-class` object
`value`	An integer matrix

Value

A matrix

A BSDMC-class object

Author(s)

Farhad Shokoohi <[email protected]>

Examples

nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
methLevels(OBJ1)
methLevels(OBJ1) <- methl
nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
methLevels(OBJ1)
methLevels(OBJ1) <- methl

methReads method

Description

Returns methReads stored in BSDMC-class

Assigns methReads to BSDMC-class

Usage

methReads(object)

methReads(object) <- value

## S4 method for signature 'BSDMC'
methReads(object)

## S4 replacement method for signature 'BSDMC,matrix'
methReads(object) <- value
methReads(object)

methReads(object) <- value

## S4 method for signature 'BSDMC'
methReads(object)

## S4 replacement method for signature 'BSDMC,matrix'
methReads(object) <- value

Arguments

`object`	A `BSDMC-class` object
`value`	An integer matrix

Value

A matrix

A BSDMC-class object

Author(s)

Farhad Shokoohi <[email protected]>

Examples

nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
methReads(OBJ1)
methReads(OBJ1) <- methc
nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
methReads(OBJ1)
methReads(OBJ1) <- methc

params

Description

parameters name and their descriptions

Arguments

`methReads`	The matrix `methReads` contains the number of methylated reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`totalReads`	The matrix `totalReads` contains the number of reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`methLevels`	The matrix `methLevels` contains the predicted methylation level spanning a CpG-site using Bayesian functional regression models. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`rowRanges`	A `GRanges` or `GRangesList` object describing the ranges of interest. Names, if present, become the row names of the `SummarizedExperiment` object. The length of the `GRanges` or `GRangesList` must equal the number of rows of the matrices in `assays`. If `rowRanges` is missing, a `SummarizedExperiment` instance is returned.
`colData`	Object of class `'DataFrame'` containing information on variable values of the samples
`metadata`	A `list` of storing MCMC samples or DMCs
`object`	A `BSDMC-class` object
`value`	An integer matrix
`name`	A character list
`obj1`	A `BSDMC-class`
`obj2`	A `BSDMC-class`
`files`	A character list
`file`	A character
`nCores`	An integer value specifying the number of machine cores for parallel computing
`mc.cores`	An integer greater than 0
`pSize`	An integer value specifying the number of cytosines in a regrion to be used in a Bayesian functiona regression model for DMC detection
`bwa`	An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the group-specific effects of the Bayesian functional regression model
`bwb`	An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the individual-specific effects of the Bayesian functional regression model
`nBurn`	An integer value specifying the number of burn-in samples
`nThin`	An integer value specifying the thining number in MCMC
`nMC`	An integer value specifying the number of MCMC samples after burn-in
`sdv`	An double value specifying the standard deviation of priors
`alpha`	A numeric value specifying the level of $\alpha$ in credible interval $(1-\alpha)\%$
`col`	A character vector indicating which colors to alternate.
`sfiles`	A logical value indicating whether files to be saved or not.
`region`	An integer vector of length two specifying which subset of the object to be plotted
`nSplit`	A integer value specifying the number of subsets must be done for plotting the results of DMC identification
`parList`	A list specifying plots parameters, see `par`
`...`	other possible parameters

Author(s)

Farhad Shokoohi <[email protected]>

plotDMCFB method

Description

Plotting the results of DMC identifation stored in a BSDMC-class object

Usage

plotDMCFB(object, region, nSplit, parList)

## S4 method for signature 'BSDMC'
plotDMCFB(object, region, nSplit, parList)
plotDMCFB(object, region, nSplit, parList)

## S4 method for signature 'BSDMC'
plotDMCFB(object, region, nSplit, parList)

Arguments

`object`	A `BSDMC-class` object
`region`	An integer vector of length two specifying which subset of the object to be plotted
`nSplit`	A integer value specifying the number of subsets must be done for plotting the results of DMC identification
`parList`	A list specifying plots parameters, see `par`

Value

Plot

Author(s)

Farhad Shokoohi <[email protected]>

Examples

set.seed(1980)
nr <- 1000
nc <- 4
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
OBJ2 <- findDMCFB(OBJ1,
  bwa = 10, bwb = 10, nBurn = 50, nMC = 50, nThin = 1,
  alpha = 0.05, nCores = 2, pSize = 500, sfiles = FALSE
)
plotDMCFB(OBJ2)
set.seed(1980)
nr <- 1000
nc <- 4
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
OBJ2 <- findDMCFB(OBJ1,
  bwa = 10, bwb = 10, nBurn = 50, nMC = 50, nThin = 1,
  alpha = 0.05, nCores = 2, pSize = 500, sfiles = FALSE
)
plotDMCFB(OBJ2)

readBismark method

Description

reads BS-Seq data

Usage

readBismark(files, colData, mc.cores)

## S4 method for signature 'character,DataFrame,numeric'
readBismark(files, colData, mc.cores)

## S4 method for signature 'character,data.frame,numeric'
readBismark(files, colData, mc.cores)

## S4 method for signature 'character,character,numeric'
readBismark(files, colData, mc.cores)
readBismark(files, colData, mc.cores)

## S4 method for signature 'character,DataFrame,numeric'
readBismark(files, colData, mc.cores)

## S4 method for signature 'character,data.frame,numeric'
readBismark(files, colData, mc.cores)

## S4 method for signature 'character,character,numeric'
readBismark(files, colData, mc.cores)

Arguments

`files`	A character list
`colData`	Object of class `'DataFrame'` containing information on variable values of the samples
`mc.cores`	An integer greater than 0

Value

A BSDMC-class object

Author(s)

Farhad Shokoohi <[email protected]>

Examples

fn <- list.files(system.file("extdata", package = "DMCFB"))
fn.f <- list.files(system.file("extdata", package = "DMCFB"),
  full.names = TRUE
)
OBJ <- readBismark(fn.f, fn, mc.cores=1)
cdOBJ <- DataFrame(Cell = factor(c("BC", "TC", "Mono"),
  labels = c("BC", "TC", "Mono")
), row.names = c("BCU1568", "BCU173", "BCU551"))
colData(OBJ) <- cdOBJ
OBJ
fn <- list.files(system.file("extdata", package = "DMCFB"))
fn.f <- list.files(system.file("extdata", package = "DMCFB"),
  full.names = TRUE
)
OBJ <- readBismark(fn.f, fn, mc.cores=1)
cdOBJ <- DataFrame(Cell = factor(c("BC", "TC", "Mono"),
  labels = c("BC", "TC", "Mono")
), row.names = c("BCU1568", "BCU173", "BCU551"))
colData(OBJ) <- cdOBJ
OBJ

totalReads method

Description

Returns totalReads stored in BSDMC-class

Assigns totalReads to BSDMC-class

Usage

totalReads(object)

totalReads(object) <- value

## S4 method for signature 'BSDMC'
totalReads(object)

## S4 replacement method for signature 'BSDMC,matrix'
totalReads(object) <- value
totalReads(object)

totalReads(object) <- value

## S4 method for signature 'BSDMC'
totalReads(object)

## S4 replacement method for signature 'BSDMC,matrix'
totalReads(object) <- value

Arguments

`object`	A `BSDMC-class` object
`value`	An integer matrix

Value

A matrix

A BSDMC-class object

Author(s)

Farhad Shokoohi <[email protected]>

Examples

nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
totalReads(OBJ1)
totalReads(OBJ1) <- metht
nr <- 150
nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
names(r1) <- 1:nr
cd1 <- DataFrame(
  Group = rep(c("G1", "G2"), each = nc / 2),
  row.names = LETTERS[1:nc]
)
OBJ1 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
totalReads(OBJ1)
totalReads(OBJ1) <- metht

Package 'DMCFB'

Help Index

Differentially Methylated cytosines using functional Bayesian regression models

Description

DMCFB methods

BSDMC objects

BSDMC object

Description

Arguments

Value

Slots

Author(s)

See Also

Examples

cBSDMC method

Description

Usage

Arguments

Details

Value

Author(s)

Examples

combine method

Description

Usage

Arguments

Value

Author(s)

Examples

findDMCFB method

Description

Usage

Arguments

Value

Author(s)

Examples

methLevels method

Description

Usage

Arguments

Value

Author(s)

Examples

methReads method

Description

Usage

Arguments

Value

Author(s)

Examples

params

Description

Arguments

Author(s)

plotDMCFB method

Description

Usage

Arguments

Value

Author(s)

Examples

readBismark method

Description

Usage

Arguments

Value

Author(s)

Examples

totalReads method

Description

Usage

Arguments

Value

Author(s)

Examples

`DMCFB` methods

`BSDMC` objects