annPeak_bytss: annPeak_bytss

Description Usage Arguments Value

View source: R/annPeak.R

Description

Annotate peak by it's nearest transcription start site. If peak overlaps multiple tss, random one will be selected.

Usage

1
annPeak_bytss(peak.gr, tx, tssup = 1000, tssdown = 1000)

Arguments

peak.gr

A peak GRanges. This can be get from Bed file of peak using bed2gr function in this package.

tx

A data frame of transcript/gene annotation, contains columns 'txid','seqnames', 'start', 'end', 'strand'.

tssup

Window size around TSS that will be defined as overlap_tss, and 0 distance will be given. Default is 1000, means must overlap within 1 kb upstream of TSS.

tssdown

Window size around TSS that will be defined as overlap_tss, and 0 distance will be given. Default is 1000, means must overlap within 1 kb downstream of TSS.

Value

A dataframe of annotated peaks with peak and it's nearest TSS information.


xons/chipMap documentation built on May 4, 2019, 1:25 p.m.