exomeCopy (version 1.18.0)

subdivideGRanges: Subdivide ranges of a GRanges object into nearly equal width ranges

Description

Takes an input GRanges object and, splits each range into multiple ranges of nearly equal width. For an input range of width w and subdividing size s, it will subdivide the range into max(1,floor(w/s)) nearly equal width ranges. The output is then a new GRanges object. This function can be used to split the targeted region (such as exons in exome enrichment experiments) into nearly equal width ranges. The ranges will be sorted and reduced if they are not already so.

Usage

subdivideGRanges(x,subsize=100)

Arguments

x

An object of type GRanges.

subsize

The desired width for the ranges in the output GRanges object.

Value

A GRanges object with ranges from the input GRanges object subdivided to nearly subsize.

See Also

GRanges

Examples

  ## read in target region BED file
  target.file <- system.file("extdata", "targets.bed", package="exomeCopy")
  target.df <- read.delim(target.file, header=FALSE,
col.names=c("seqname","start","end")) 

  ## create GRanges object with 5 ranges over 2 sequences
  target <- GRanges(seqname=target.df$seqname,
               IRanges(start=target.df$start,end=target.df$end))

  ## subdivide into 7 smaller genomic ranges
  target.sub <- subdivideGRanges(target)