Remove extraneous/unused code - Githubissues

Huntsmanlab / utanos

Utilities for doing analysis on shallow WGS data

https://huntsmanlab.github.io/utanos/

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Remove extraneous/unused code #62

Open brandenjlynch opened 3 months ago

brandenjlynch commented 3 months ago

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[ ] When ready, remove the nearly outdated quickstart vignette as it has mostly been made redundant.

genomaxx commented 1 month ago

First 5 of those redundant functions we've found removed in my current branch. Will be included in next PR.