crosscoverage-methods {ChIPQC} | R Documentation

## Retrieve the cross coverage values for a range of shift sizes

### 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)

[Package ChIPQC version 1.16.1 Index]