trimGRanges: trim GRanges object

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

trim GRanges object

Description

trim to get the first or last bases from GRanges.

Usage

  trimGRanges(x, width = 100, start = TRUE)

Arguments

x	A GRanges object.
width	integer(1): the length of bases to fetch.
start	logical(1): fetch from the start or end.

Details

Image we have exons from the same transcript in the x. We want to fetch 100 bases of CDS from 5' end or 3' end.

Value

A GRanges object.

Author(s)

Ge Tan

Examples

  gr <- GRanges(seqnames="chr1",
                ranges=IRanges(start=c(2,10,20),
                               end=c(5, 15, 23)),
                strand="+")
  trimGRanges(gr, width=3, start=TRUE)
  trimGRanges(gr, width=4, start=TRUE)
  trimGRanges(gr, width=11, start=TRUE)
  trimGRanges(gr, width=11, start=FALSE)

uzh/ezRun documentation built on April 24, 2024, 4:01 p.m.