generateBackground: Generate median background read depth

Description Usage Arguments Value Examples

View source: R/helper_functions.R

Description

Normalizes a set of columns representing read counts from different samples by their mean. Then calculates a statistic across the rows of normalized counts.

Usage

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  generateBackground(sample.names, gr, fn=median)

Arguments

sample.names

A vector of metadata column names in gr to be used as background samples

gr

A GRanges object containing the read counts

fn

The statistic to be applied across the rows of normalized counts. Defaults to median, but the standard deviation can also be calculated in this way.

Value

The value of fn applied across the rows of normalized read counts.

Examples

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  data(exomecounts)
  sample.names <- grep("HG.+",colnames(mcols(exomecounts)),value=TRUE)
  exomecounts$bg <- generateBackground(sample.names, exomecounts, median) 
  exomecounts$bg.sd <- generateBackground(sample.names, exomecounts, sd) 

exomeCopy documentation built on Nov. 17, 2017, 8:34 a.m.