TransView (version 1.16.0)

annotatePeaks: Associates peaks to TSS

Description

A convenience function to associate the peak center to a TSS or gene body provided by a gtf file.

Usage

annotatePeaks(peaks, gtf, limit=c(-10e3,10e3), remove_unmatched=T, unifyBy=F, unify_fun="mean", min_genelength=0, reference="tss")

Arguments

peaks

A GRanges object.

gtf

A GRanges object with a meta data column ‘transcript_id’ and ‘exon_id’ like e.g. from gtf2gr.

limit

Maximal distance range for a peak - TSS association in base pairs.

remove_unmatched

If TRUE, only TSS associated peaks will be returned.

unifyBy

If a transcript has multiple isoforms, the peak will be associated arbitrarily to the first ID found. In order associate a peak to an isoform with specific characteristics, a DensityContainer can be provided. The choice of the returned isoform will be made based on unify_fun.

unify_fun

A function which will choose the isoform in case of non unique peak - TSS associations. Defaults to the isoform with the highest mean score function(x){mean(x)}.

min_genelength

Genes with a total sum of all exons smaller than this value will not be associated to a peak.

reference

If set to ‘tss’, the transcript with the smallest distance from the TSS to the peak center will be returned. If set to ‘gene_body’ the transcript with the smallest distance from the gene body (TSS or TES) to the peak center will be returned and the distance will be zero if the peak center is located within the gene body.

Value

GRanges object with row names according to the peak names provided and an added or updated meta data column ‘transcript_id’ with the associated transcript IDs and distances.

Details

Convenience function to annotate a GRanges object having one row per peak from e.g. macs2gr. The resulting peak - TSS associations can be customized by the restricting the distance and resolving multiple matches using unify_fun.

Examples

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

GTF<-gtf2gr(exgtf)
peaks<-macs2gr(exls,psize=500)
apeaks<-annotatePeaks(peaks=peaks,gtf=GTF)
apeaks.gb<-annotatePeaks(peaks=peaks,gtf=GTF,reference="gene_body")