Description Usage Arguments Value Examples
This function plots the raw read information from the location of interest for a trio.
1 | visualizeDeletion(deletion, bins, metaData, mCounts, md, save = FALSE)
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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.
1 2 3 4 5 6 7 8 9 10 11 | ## 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)
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