visualizeDeletion: Visualization for deletions

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

Description

This function plots the raw read information from the location of interest for a trio.

Usage

visualizeDeletion(deletion, bins, metaData, mCounts, md, save = FALSE)

Arguments

deletion	A GRanges object in the format of the output of denovoDeletions().
bins	The set of bins determined by calcBins().
metaData	A table in the format of the output of getMetaData().
mCounts	A matrix of normalized coverage output by normalizedCounts().
md	The minimum distance matrix output by calcMD()
save	If TRUE will save plot to current working directory instead of rendering.

Value

The file name if the plot was saved.

Examples

## Not run: 
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)
visualizeDeletion(denovo[1], bins, pD, mCounts, md)

## End(Not run)

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