Huntsmanlab / utanos

Utilities for doing analysis on shallow WGS data
https://huntsmanlab.github.io/utanos/
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Plot cn with genes #46

Closed brandenjlynch closed 1 year ago

brandenjlynch commented 1 year ago

Created a new function to add genes of interest to absolute copy-number plots. Updated documentation. Tweaked an existing test to determine the path to the test fixtures in a robust way, rather than via a relative path which fails under some testing circumstances.

One potential area of contention in the AddGenesToPlot function is the handling of genome versions. Right now, rather than force the inclusion of additional annotation packages for other genome versions, I am defaulting to EnsDb.Hsapiens.v75, which is already required. If desired, a user can supply an arbitrary Ensembl package to use for annotation. We could consider asking for a genome build and determining the annotation package based on that, but it would necessitate including a different annotation package or using something like BioMart.

Alternatively we could decouple the gene annotation process entirely and require the user to supply a table of gene names, along with their locations (chromosome, start, end). That doesn't seem very user-friendly, so I opted for the current approach, but it would enable this function to label anything (gene, micro-satellite, whatever) according to its genomic location.

genomaxx commented 1 year ago

That seems reasonable to me re: ref genome. I think at some point EnsDb.Hsapiens.v86 is going to become a requirement given the number of different places in this package where we make use of a reference genome though.

genomaxx commented 1 year ago

Not a huge fan of yet another dependency but I think that one would be reasonable.

genomaxx commented 1 year ago

Code-wise things look good, thanks for including good roxygen docs!