generateBackground: Generate median background read depth
In exomeCopy: Copy number variant detection from exome sequencing read depth

Description Usage Arguments Value Examples

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

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

`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.

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

  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)