Package 'ChIPexoQual'

ARCvURCplot

Description

ARCvURCplot returns a ggplot object with the ARC vs URC plot to analyze enrichment and library complexity in ChIP-exo data.

Usage

ARCvURCplot(..., names.input = NULL, both.strand = FALSE)

Arguments

...	a list of ExoData objects, or several ExoData objects by themselves.
names.input	a character vector with the names to use in the plot. If it is empty ARCvURCplot is going to create the names as the names of the list when they are available or is going to name them as Sample: 1 ,... , Sample: k.
both.strand	A logical value indicating if the DataFrame contains only regions with reads aligned to both strand or all. The default value is FALSE.

Value

A ggplot2 object with the ARC vs URC plot.

Examples

data(exoExample)
ARCvURCplot(exoExample)

---

beta1 methods

Description

beta1 returns a vector with all the estimated values of the $d_i = \beta_1 u_i + \beta_2 w_i + \epsilon_i$ models fitted by ChIPexoQual

Usage

beta1(object)

## S4 method for signature 'ExoData'
beta1(object)

Arguments

object

a ExoData object.

Value

A numeric vector with estimated values for $\beta_1$.

Examples

data(exoExample)
beta1(exoExample)

---

beta2 methods

Description

beta2 returns a vector with all the estimated values of the $d_i = \beta1 u_i + \beta2 w_i + \epsilon_i$ models fitted by ChIPexoQual

Usage

beta2(object)

## S4 method for signature 'ExoData'
beta2(object)

Arguments

object

a ExoData object.

Value

A numeric vector with estimated values for $\beta_2$.

Examples

data(exoExample)
beta2(exoExample)

---

list of GRanges objects with the blacklists generated by the ENCODE and modENCODE projects.

Description

list of GRanges objects with the blacklists generated by the ENCODE and modENCODE projects.

Usage

data(blacklists)

Format

list of GRanges objects.

Value

A list with the blacklists listed in https://sites.google.com/site/anshulkundaje/projects/blacklists.

---

calculateParamDist calculateParamDist calculates the quality parameters of one iteration. This function samples nregions rows from the stat matrix and fits the linear model lm(d ~ 0 + u + w)

Description

calculateParamDist

calculateParamDist calculates the quality parameters of one iteration. This function samples nregions rows from the stat matrix and fits the linear model lm(d ~ 0 + u + w)

Usage

calculateParamDist(i, stats, nregions)

Arguments

i	a numeric value indicating the current iteration.
stats	a data.table object with the response and covariates for the model
nregions	a numeric value indicating the number of regions sampled.

Value

a data.table with both parameters and some extra info

Examples

data("exoExample")
DT <- formatRegions(exoExample)
calculateParamDist(1,DT,100)

---

ExoData object and constructors

Description

ExoData is a subclass of GenomicRanges, used to asses the quality of ChIP-exo/nexus sample.

Usage

ExoData(file = NULL, reads = NULL, height = 1,
  mc.cores = getOption("mc.cores", 2L), save.reads = FALSE,
  nregions = 1000, ntimes = 100, verbose = TRUE)

Arguments

file	a character value with location of the bam file with the aligned reads.
reads	a GAlignments object with the aligned reads of a ChIP-exo sample. It is meant to be used instead of file.
height	a numeric value indicating the value used to slice the coverage of the experiment into a set of regions.
mc.cores	a numeric value with the number of cores to use, i.e. at most how many child processes will be run simultaneously.
save.reads	a logical value to indicate if the reads are stored in the ExoData object. The default value is FALSE.
nregions	a numeric value indicating the number of regions sampled to estimate the quality parameter distributions. The default value is 1e3.
ntimes	a numeric value indicating the number of times that regions are sampled to estimate the quality parameter distributions. The default value is 1e2.
verbose	a logical value indicating if the user want to receive progress details. The default value is FALSE.

Value

It returns an ExoData object with the regions obtained after partitioning the genome and the summary statistics for each region. If the save.reads parameter is TRUE then it contains a GRanges object with the reads of the ChIP-exo experiment.

Examples

files <- list.files(system.file("extdata",package = "ChIPexoQualExample"),
    full.names = TRUE)
ExoData(files[5],mc.cores = 2L)

---

ExoDataBlacklist

Description

ExoDataBlacklist separates the regions in an ExoData object by overlapping them with a set of blacklisted regions and calculates the quality parameters in both collections of islands.

Usage

ExoDataBlacklist(exo, blacklist, which.param = "beta1", nregions = NULL,
  ntimes = NULL)

Arguments

exo	a ExoData object.
blacklist	a GRanges object with the blacklisted regions or a character indicating which of the blacklist included in ChIPexoQual to use.
which.param	a character value with either "beta1" or "beta2" that determines which parameters in the model depth_i ~ uniquePos_i + width_i to plot. The default value is "beta1".
nregions	a numeric value indicating the number of regions sampled to estimate the quality parameter distributions. The default value is extracted from exo.
ntimes	a numeric value indicating the number of times that regions are sampled to estimate the quality parameter distributions. The default value is extracted from object.

Value

A ggplot object with a boxplot that compares the quality scores distribution when the regions overlap a pre-defined collection of blacklists.

Examples

data(exoExample)
data(blacklists)
ExoDataBlacklist(exoExample,blacklists[["mm9"]],ntimes = 10,nregions = 500)

---

ExoDataSubsampling

Description

ExoDataSubsampling samples sample.reads from the ChIP-exo experiment and creates a list of ExoData objects

Usage

ExoDataSubsampling(file = NULL, reads = NULL, sample.depth = NULL,
  height = 1, nregions = 1000, ntimes = 1000, verbose = TRUE,
  save.reads = FALSE, mc.cores = getOption("mc.cores", 2L))

Arguments

file	a character value with location of the bam file with the aligned reads.
reads	a GAlignments object with the aligned reads of a ChIP-exo sample. It is meant to be used instead of file.
sample.depth	a numeric vector with the number of reads to be sampled.
height	a numeric value indicating the value used to slice the coverage of the experiment into a set of regions.
nregions	a numeric value indicating the number of regions sampled to estimate the quality parameter distributions. The default value is 1e3.
ntimes	a numeric value indicating the number of times that regions are sampled to estimate the quality parameter distributions. The default value is 1e2.
verbose	a logical value indicating if the user want to receive progress details. The default value is FALSE.
save.reads	a logical value to indicate if the reads are stored in the ExoData object. The default value is FALSE.
mc.cores	a numeric value with the number of cores to use, i.e. at most how many child processes will be run simultaneously.

Value

It returns an ExoData object with the regions obtained after partitioning the genome and the summary statistics for each region. If the save.reads parameter is TRUE then it contains a GRanges object with the reads of the ChIP-exo experiment.

Examples

files <- list.files(system.file("extdata",package = "ChIPexoQualExample"),
    full.names = TRUE)
sample.depth <- seq(1e5,2e5,5e4)
ExoDataSubsampling(file = files[5],sample.depth = sample.depth)

---

ExoData results for FoxA1 ChIP-exo experiment

Description

ExoData object, generated with ChIPexoQual and the file:

Usage

data(exoExample)

Format

ExoData object, which are GRanges with additional columns.

Details

• ChIPexo_carroll_FoxA1_mouse_rep3_chr1.bam

Value

An ExoData object with the 3rd replicate of the FoxA1 experiment from ChIPExoQualExample.

---

formatRegions formatRegions separates the width, depth and uniquePos summary statistics from the ExoData object to calculate the quality parameters/

Description

formatRegions

formatRegions separates the width, depth and uniquePos summary statistics from the ExoData object to calculate the quality parameters/

Usage

formatRegions(exo)

Arguments

exo	a ExoData object

Value

a data.table with the width, depth and uniquePos of the regions in exo.

Examples

data("exoExample")
formatRegions(exoExample)

---

FSRDistplot

Description

FSRDistplot returns a ggplot object with the Forward Strand Ratio distribution plot to analyze strand imbalance in ChIP-exo data.

Usage

FSRDistplot(..., names.input = NULL, quantiles = c(0, 0.25, 0.5, 0.75, 1),
  depth.values = seq_len(30), both.strand = FALSE)

Arguments

...	a list of ExoData objects, or several ExoData objects by themselves.
names.input	a character vector with the names to use in the plot. If it is empty FSRDistplot is going to create the names as the names of the list when they are available or is going to name them as Sample: 1 ,... , Sample: k.
quantiles	a numeric vector with the quantiles used to estimate the FSR distribution at a given depth. The default value is c(0,.25,.5,.75,1))
depth.values	a numeric vector indicating the regions with depth less or equal to, that are going to be filtered out. The defaulta values are seq_len(50).
both.strand	a logical value indicating if the DataFrame contains only regions with reads aligned to both strand or all. The default value is FALSE.

Value

A ggplot2 object with the FSR distribution plot.

Examples

data(exoExample)
FSRDistplot(exoExample)

---

MAplot

Description

MAplot returns a ggplot object with the MA plot to analyze the strand imbalance in ChIP-exo data.

Usage

MAplot(..., names.input = NULL)

Arguments

...	a list of ExoData objects, or several ExoData objects by themselves.
names.input	a character vector with the names to use in the plot. If it is empty MAplot is going to create the names as the names of the list when they are available or is going to name them as Sample: 1 ,... , Sample: k.

Value

A ggplot2 object with the MA plot.

Examples

data(exoExample)
MAplot(exoExample)

---

nreads methods

Description

nreads returns the number of reads in the object.

Usage

nreads(object)

## S4 method for signature 'ExoData'
nreads(object)

Arguments

object

A ExoData object.

Value

The number of reads in the ExoData object.

Examples

data(exoExample)
nreads(exoExample)

---

paramDist methods

Description

paramDist returns a DataFrame with all the estimated coefficients in the $d_i = \beta_1 u_i + \beta_2 w_i + \epsilon_i$ models fitted by ChIPexoQual

Usage

paramDist(object)

## S4 method for signature 'ExoData'
paramDist(object = "ExoData")

Arguments

object

a ExoData object.

Value

A DataFrame with the fitted values of $\beta_1$ and $\beta_2$.

Examples

data(exoExample)
paramDist(exoExample)

---

paramDistBoxplot

Description

paramDistBoxplot returns a ggplot object with a boxplot comparing the ntimes estimations of the chosen parameter.

Usage

paramDistBoxplot(..., names.input = NULL, which.param = "beta1",
  sort.as.numeric = FALSE)

Arguments

...	a list of ExoData objects, or several ExoData objects by themselves.
names.input	a character vector with the names to use in the plot. If it is empty paramDistBoxplot is going to create the names as the names of the list when they are available or is going to name them as Sample: 1 ,... , Sample: k.
which.param	a character value with either "beta1" or "beta2" that determines which paramters in the model depth_i ~ uniquePos_i + width_i to plot. The default value is "beta1".
sort.as.numeric	a logical value indicating if the values of names.input are meant to be interpreted as numeric and sorted accordingly.

Value

A ggplot2 object with the boxplot of the chosen parameter

Examples

data(exoExample)
paramDistBoxplot(exoExample)

---

regionCompplot

Description

regionCompplot returns a ggplot object with the Region Composition plot to analyze strand imbalance in ChIP-exo data.

Usage

regionCompplot(..., names.input = NULL, depth.values = seq_len(15))

Arguments

...	a list of ExoData objects, or several ExoData objects by themselves.
names.input	a character vector with the names to use in the plot. If it is empty regionCompplot is going to create the names as the names of the list when they are available or is going to name them as Sample: 1 ,... , Sample: k.
depth.values	a numeric vector indicating the regions with depth less or equal to, that are going to be filtered out. The defaulta values are seq_len(50).

Value

A ggplot2 object with the Region Composition plot.

Examples

data(exoExample)
regionCompplot(exoExample)

---