visualizeDeletion: Visualization for deletions

Description Usage Arguments Value Examples

View source: R/visualizeDeletion.R

Description

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

Usage

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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

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## 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/MDTS documentation built on May 28, 2019, 12:42 p.m.