coveragehistogram-methods {ChIPQC} | R Documentation

## Retrieve histogram data representing densities of coverage pileups

### Description

Retrieve histogram data representing densities of coverage pileups.

### Methods

`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.

### Author(s)

Thomas Carroll and Rory Stark

### See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

### Examples

    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)

[Package ChIPQC version 1.28.0 Index]