segmentMD: Circular Binary Segmentation on Minimum Distances

In JMF47/DnMD: Detection of de novo deletion in targeted sequencing trios

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

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

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)

JMF47/DnMD documentation built on May 31, 2019, 10:44 p.m.