annotatePeaks: Associates peaks to TSS

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

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.

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.

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.

Author(s)

Julius Muller [e-mail]

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")

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