There are a few functions which are overly-specific to one dataset and hence lack a general use case. These, and other obsolete functions should potentially be removed:
[x] SampleGrouping() in samplequality.R
[x] PlotCellularityAndMaxVaf() in plotting.R
[x] PlotBABAM() in plotting.R
[x] PlotMetadataHeatmaps() in plotting.R
[x] AddViralPresence() in plotting.R
These may be removed, pending updates that replace them/testing:
[ ] SummaryCNPlot in plotting.R
[ ] RelativeCNSegmentsPlot in plotting.R
Files:
[ ] When ready, remove the nearly outdated quickstart vignette as it has mostly been made redundant.
There are a few functions which are overly-specific to one dataset and hence lack a general use case. These, and other obsolete functions should potentially be removed:
These may be removed, pending updates that replace them/testing:
Files: