denovoDeletions {MDTS}R Documentation

Denovo Deletion Calling

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)

[Package MDTS version 1.14.0 Index]