peak2tss: Changes the peak center to the next TSS according to previous...

In TransView: Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Description

Sets the peak boundaries of an annotated GRanges object with peak locations to TSS centered ranges based on the transcript_id column.

Usage

peak2tss(peaks, gtf, peak_len=500)

Arguments

peaks	An annotated GRanges object with a meta data column ‘transcript_id’ and ‘exon_id’ like e.g. from gtf2gr.
gtf	A GRanges object with a meta data column ‘transcript_id’ like e.g. from annotatePeaks.
peak_len	The desired total size of the region with the TSS located in the middle.

Details

Convenience function to change the peak centers to TSS for e.g. plotting with plotTV.

Value

A GRanges object

Author(s)

Julius Muller [e-mail]

Examples

exgtf<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="gtf.gz$")[2]
fn.macs<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="xls$")

GTF<-gtf2gr(exgtf)
peaks<-macs2gr(fn.macs,psize=500)

peaks.anno<-annotatePeaks(peaks=peaks,gtf=GTF)

peak2tss(peaks.anno, GTF, peak_len=500)

TransView documentation built on Nov. 8, 2020, 5:31 p.m.