normalizeCounts: Calculating the normalized M scores

Description Usage Arguments Value Examples

View source: R/normalizeCounts.R

Description

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

Usage

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normalizeCounts(counts, bins, GC = TRUE, map = TRUE, mc.cores = 1)

Arguments

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.

Value

A data.frame of normalized counts. Each column is a sample, and each row is a entry of bins.

Examples

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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)

MDTS documentation built on Nov. 1, 2018, 2:24 a.m.