visualizeDeletion {MDTS} | R Documentation |
This function plots the raw read information from the location of interest for a trio.
visualizeDeletion(deletion, bins, metaData, mCounts, md, save = FALSE)
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. |
The file name if the plot was saved.
## 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)