normalizeCounts: Calculating the normalized M scores
In JMF47/DnMD: Detection of de novo deletion in targeted sequencing trios

Description Usage Arguments Value Examples

This function will return a matrix of normalized M scores where ecah column is a sample, and each row is a bin.

1	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)