averagepeaksignal-methods: Retrieve average peak profiles

In shengqh/ChIPQC: Quality metrics for ChIPseq data

Retrieve average peak profiles

Description

Retrieve the average peak profile for a sample or set of samples.

Methods

signature(object = "ChIPQCexperiment")

Retrieve a matrix of the average peak profiles for all of the samples in an ChIP-seq experiment. Each column represents a sample, and each row a base pair position, centered on peak summits.

signature(object = "list")

Retrieve a matrix of the average peak profiles for all of the samples in a list of ChIPQC samples. Each column represents a sample, and each row a base pair position, centered on peak summits.

signature(object = "ChIPQCsample")

Retrieve a vector representing the average peak profile for a sample. Each column represents a basepair position, centered on the peak summits.

Author(s)

Thomas Carroll and Rory Stark

See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

Examples

data(example_QCexperiment)
CTCFprofile = averagepeaksignal(QCsample(exampleExp,1))
length(CTCFprofile)
plot(CTCFprofile,type='l',ylab="mean pileup")

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

shengqh/ChIPQC documentation built on Feb. 27, 2023, 10:51 p.m.