peak_merge {primirTSS}R Documentation

Merge adjacent peaks within H3K4me3 or Pol II data.

Description

Merge the adjacent segments provided as GRange object from original data. This function will merge adjacent peaks the distance between which is less than n base pairs apart and then return the merged segments.

Usage

peak_merge(peak, n = 250)

Arguments

peak

A GRange object. The peaks to be merged from one certain ChIP-seq data, such as H3K4me3 data or Pol II data.

n

A number. n stipulates the distance(bp, base pair) between two seperate peaks within which they should be merged.

Value

A GRanges object. The merged peaks for the following analysis to search for TSSs.

Examples

peak_df <- data.frame(chrom = c("chr1", "chr2", "chr1"),
                      chromStart = c(450, 460, 680),
                      chromEnd = c(470, 480, 710),
                      stringsAsFactors = FALSE)
peak <-  as(peak_df, "GRanges")

peak_merge(peak, n =250)
[Package primirTSS version 1.0.1 Index]