normalizeCounts {MDTS} | R Documentation |
This function will return a matrix of normalized M scores where ecah column is a sample, and each row is a bin.
normalizeCounts(counts, bins, GC = TRUE, map = TRUE, mc.cores = 1)
counts |
A matrix of raw coverage output by calcCounts(). |
bins |
The set of bins determined by calcBins(). |
GC |
Whether to loess adjust for GC. Defaults to TRUE. |
map |
Whether to loess adjust for mappability. Defaults to TRUE. Defaults to 1. |
mc.cores |
The number of cores to use for multi-threaded analysis. |
A data.frame
of normalized counts. Each column is a sample,
and each row is a entry of bins
.
load(system.file("extdata", 'bins.RData', package = "MDTS")) load(system.file("extdata", 'counts.RData', package = "MDTS")) load(system.file("extdata", 'pD.RData', package = "MDTS")) mCounts <- normalizeCounts(counts, bins)