getAlts: getAlts

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

Description

takes a data frame of segments and extracts just those containing copy-number gains and losses (that exceed the gain/loss thresholds)

Usage

  getAlts(segs,rdo)

Arguments

segs	a data frame that is the result of calling rd.cnSegments
rdo	a readDepth object created with new("rdObject")

Value

a data frame containing only segments of CN gain and loss

See Also

'rd.cnSegments'

Examples

  ##get regions of CN gain and loss
  #  segs <- rd.cnSegments(x)

  ##extract just the gains and losses
  #  alts <- getAlts(segs,x)

chrisamiller/readDepth documentation built on June 16, 2021, 2:05 p.m.