trimSegmentEnds: trimSegmentEnds

In chrisamiller/copyCat: Find regions of genomic copy number loss and gain from short reads

Description

trim the ends of segments such that they're called normal (CN = 2.0) until the first bin that isn't NA

useful for chromosomes like 22, where there are tens of megabases that are unmappable at beginning. Without this, those regions would be called with the same CN as the first few mappable bins. This may or may not be desirable behavior, so use with caution

Usage

  trimSegmentEnds(segs, rdo)

Arguments

segs	a data frame that is the result of calling cnSegments()
rdo	a read depth object

Value

the segment data frame adjusted to have the ends trimmed

Examples

  ##get regions of CN gain and loss
  #  segs <- cnSegments(rdo)

  ##trim the segment ends 
  #  trimSegmentEnds(segs, rdo)

chrisamiller/copyCat documentation built on July 20, 2021, 12:59 a.m.