subtractBins: subtractBins

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

Description

takes two rd objects, and subtracts the read depth in each bin from the second from the first (using the rd column)

Usage

  subtractBins(rdo,rdo2,normalization=FALSE)

Arguments

rdo	a readDepth object
rdo2	a readDepth object
normalization	do normalization of the read counts

Value

an rd object identical to the first rd object, except that the read depth in the rd column is the difference between the rd columns from the two objects.

Examples

  ##create a rdObject, set bin params
  # x <- new("rdObject")

  ##fill the bins with reads
  # x <- getReadDepth(x)

  ##create a rdObject, set bin params
  # y <- new("rdObject")

  ##fill the bins with reads
  # y <- getReadDepth(y)

  ##sum the rd columns
  # x <- subtractBins(x,y)

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