gcCorrect: readDepth: GC-content correction

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

Description

takes a readDepth object containing read counts and uses loess correction to account for GC content bias. Updates the @chrs rd column and adds a "gc" column containing that bin's GC content percentage

Usage

  gcCorrect(rdo, meth=FALSE, outlierPercentage=0.01, resolution = 0.001)

Arguments

rdo	a readDepth object created with new("rdObject") and filled with read counts using the readDepth() command
meth	if this data consists of bisulfite reads and a methylation map is present in annotations/methMap, gc correction will be done while taking into account the bisulfite treatment that converts C -> U and methylated bases that were protected from this conversion
outlierPercentage	Removes the highest and lowest N% of reads before loess correction This prevents overfitting near the extremes, to which loess is susceptible. Default value is 0.01
resolution	the resolution at which to bin the values (0.01=1%)

Details

Assumes that appropriate annotation files are in place (see full copyCat documentation for more information).

Value

returns a rd object with the read depth values altered to reflect gc content composition-induced bias.

See Also

'getReadDepth'

Examples

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

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

  ##do gc correction on the read counts
  #  x.gcCorr = gcCorrect(x)

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