rd.mapCorrect: Correct read depth for unmappable regions

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

Description

takes a readDepth object containing read counts and updates the rd counts, account for repetitive and unmappable genomic regions. Also adds a "map" column containing that bin's percentage mapability

Usage

  rd.mapCorrect(rdo, minMapability=0.25)

Arguments

rdo	a readDepth object created with new("rdObject") and filled with read counts using the readDepth() command
minMapability	the minimum amount of mapability required. If the mapability of a region is below this level, the read depth is set to NA.

Details

Assumes that files containing unmappable regions are in place (see readDepth documentation for proper directory structure).

Value

returns a readDepth object with the read depth values altered to remove bias due to mappability

See Also

'readDepth'

Examples

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

  ##fill the bins with reads
  #  x.reads <- readDepth(x)

  ##do mapping correction on the read counts
  #  x.mapCorr = rd.mapCorrect(x.reads)

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