peak2tss {TransView} | R Documentation |
Sets the peak boundaries of an annotated GRanges object with peak locations to TSS centered ranges based on the transcript_id column.
peak2tss(peaks, gtf, peak_len=500)
peaks |
An annotated GRanges object with a meta data column ‘transcript_id’ and ‘exon_id’ like e.g. from |
gtf |
A GRanges object with a meta data column ‘transcript_id’ like e.g. from |
peak_len |
The desired total size of the region with the TSS located in the middle. |
Convenience function to change the peak centers to TSS for e.g. plotting with plotTV
.
A GRanges object
Julius Muller ju-mu@alumni.ethz.ch
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)