crosscoverage-methods: Retrieve the cross coverage values for a range of shift sizes

In ChIPQC: Quality metrics for ChIPseq data

Description

Retrieves the cross-coverage values for a range of shift sizes.

Methods

signature(object = "ChIPQCexperiment")

Retrieve a matrix of cross-coverage data for all samples in an ChIP-seq experiment. Each column represents a sample, and each row a shift size, with the value representing the cross-coverage using that size read.

signature(object = "list")

Retrieve a matrix of cross-coverage data for all samples in a list of ChIPQCsample objects. Each column represents a sample, and each row a shift size, with the value representing the cross-coverage using that size read.

signature(object = "ChIPQCsample")

Retrieve a vector of cross-coverage data for a sample. Each position in the vector corresponds to a shift size, with the value representing the cross-coverage using that size read.

Author(s)

Thomas Carroll and Rory Stark

See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

Examples

data(example_QCexperiment)
CTCFcoverage = crosscoverage(QCsample(exampleExp,1))
length(CTCFcoverage)
plot(CTCFcoverage,type='l',
     ylab="Cross-coverage",
     xlab="Fragment length") 

allcoverages = crosscoverage(exampleExp)
dim(allcoverages)
for(i in 1:ncol(allcoverages)) lines(allcoverages[,i],col=i)

ChIPQC documentation built on Nov. 8, 2020, 8:06 p.m.