denovoDeletions: Denovo Deletion Calling

Description Usage Arguments Value Examples

View source: R/denovoDeletions.R

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

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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

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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)
denovo = denovoDeletions(cbs, mCounts, bins)

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