\name{averagepeaksignal-methods} \docType{methods} \alias{averagepeaksignal} \alias{averagepeaksignal-methods} \alias{averagepeaksignal,ChIPQCexperiment-method} \alias{averagepeaksignal,ChIPQCsample-method} \alias{averagepeaksignal,list-method} \title{Retrieve average peak profiles} \description{ Retrieve the average peak profile for a sample or set of samples. } \section{Methods}{ \describe{ \item{\code{signature(object = "ChIPQCexperiment")}}{ Retrieve a \code{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. } \item{\code{signature(object = "list")}}{ Retrieve a \code{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. } \item{\code{signature(object = "ChIPQCsample")}}{ Retrieve a \code{vector} representing the average peak profile for a sample. Each column represents a basepair position, centered on the peak summits. } }} \keyword{methods} \author{Thomas Carroll and Rory Stark} \seealso{ \link{ChIPQC-package}, \link{ChIPQCexperiment}, \link{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) }