coveragehistogram-methods: Retrieve histogram data representing densities of coverage...
In ChIPQC: Quality metrics for ChIPseq data

Description Methods Author(s) See Also Examples

Retrieve histogram data representing densities of coverage pileups.

signature(object = "ChIPQCexperiment"): Retrieve a matrix of coverage histogram data for all samples in a ChIP-seq experiment. Each column represents a sample, and each row a pileup height, with the value representing the number of basepair positions that report this pileup height.
signature(object = "list"): Retrieve a matrix of coverage histogram data for all ChIPQCsamples in a list. Each column represents a sample, and each row a pileup height, with the value representing the number of basepair positions that report this pileup height.
signature(object = "ChIPQCsample"): Retrieve a vector representing coverage histogram data for a sample. Values represent the number of base pairs positions that report the pileup value. The value in position 1 of the vector the contains the number of examined basepair positions that are overlapped by exactly zero reads, while position 2 shows the number of basepair positions overlapped by exactly one read, etc.

Thomas Carroll and Rory Stark

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

data(example_QCexperiment)
CTCFcoverage = coveragehistogram(QCsample(exampleExp,1))
length(CTCFcoverage)
plot(log10(CTCFcoverage),type='l',ylab="log10 Density",
                          xlab="Pileup")

allcoverages = coveragehistogram(exampleExp)
dim(allcoverages)
for(i in 1:ncol(allcoverages)) lines(log10(allcoverages[,i]),col=i)