nearest_peak: nearest_peak

Description Usage Arguments Value

View source: R/annPeak.R

Description

Find nearest peak of given genes's transcription start site. If tss overlaps multiple peaks, random one will be selected.

Usage

1
nearest_peak(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.

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 with gene and it's nearest peak information.


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