denovoDeletions: Denovo Deletion Calling

In MDTS: Detection of de novo deletion in targeted sequencing trios

Description

This function will return a single GRanges object containing all denovo deletions that passed filtering from a Circular Binary Segmentation object with supplementary information.

Usage

denovoDeletions(cbs, mCounts, bins)

Arguments

cbs	The output from segmentMD().
mCounts	The normalized counts matrix output by normalizeCounts().
bins	The set of bins determined by calcBins().

Value

A GRanges object that reports all detected denovo deletions passing requite filters.

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)
denovo = denovoDeletions(cbs, mCounts, bins)

MDTS documentation built on Nov. 8, 2020, 6:23 p.m.