generateBackground {exomeCopy} | R Documentation |
Normalizes a set of columns representing read counts from different samples by their mean. Then calculates a statistic across the rows of normalized counts.
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)