segmentMD: Circular Binary Segmentation on Minimum Distances

Description Usage Arguments Value Examples

View source: R/segmentMD.R

Description

This function will return a GRanges object containing the copy number segments of all families in the input minimum distance matrix. It calls segment() from DNAcopy (alpha=0.001, undo.splits="sdundo", undo.SD=4).

Usage

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segmentMD(md, bins, alpha = 0.001, undo.splits = "sdundo", undo.SD = 4,
  mc.cores = 1)

Arguments

md

The minimum distance matrix produced by calcMD.

bins

The set of bins determined by calcBins.

alpha

Controls the alpha option in calling DNAcopy::segment()

undo.splits

Controls the undo.splits option in DNAcopy::segment()

undo.SD

Controls the undo.SD option in calling DNAcopy::segment()

mc.cores

The number of cores to use for multi-threaded analysis. Defaults to 1.

Value

A data.frame containing the segmented regions based to be parsed by denovoDeletions() minimum distance.

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)
md <- calcMD(mCounts, pD)
cbs <- segmentMD(md, bins)

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