reduceByPercentage: Reduce by percentage of overlaps of GRanges object

In jianhong/ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq

Reduce by percentage of overlaps of GRanges object

Description

Merge the ranges by percentage of overlaps to avoid broad ranges of continues ranges overlapped with limit bases.

Usage

reduceByPercentage(
  query,
  percentage,
  ignore.strand = TRUE,
  colnToKeep = c("score", "motif")
)

Arguments

query	An object of GRanges
percentage	A numeric vector (length=1). The percentage of overlapping region of binding sites to merge as one range.
ignore.strand	When set to TRUE, the strand information is ignored in the calculations.
colnToKeep	The metadata colnums should be kept for reduced GRanges

Value

An object of GRanges.

Examples

library(GenomicRanges)
gr <- GRanges("chr1", IRanges(c(1, 5, 10), width=c(10, 5, 2)))
reduceByPercentage(gr, 0.5, colnToKeep=NULL)

jianhong/ATACseqTFEA documentation built on Feb. 9, 2024, 4:09 a.m.