gnomeR

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For example, gene correlations – user gets to pick which genes to correlate (not sure what the current selection process is)

hfuchs5

From Caroline: I’ve been considering working on these sorts of functions/smoothing out this pipeline for my own personal use. Happy to share when complete if they belong in gnomeR or...

hfuchs5

Functions like `summarize_by_gene()`, `susbet_by_frequency()` and `tbl_genomic()` all require a binary matrix input. These all have internal checks but we should synthesize into one input checking function (maybe `.check_gene_binary()` or `sanitize_gene_binary()`)....

karissawhiting

"LOSS" not accepted as an alteration type for pivot_cna_wider

1

 repex crc_pub % pivot_cna_wider()

hfuchs5

Per Karissa: comparing the fusion files there are some genes with new names. We need more unit tests to make sure that this is correctly done

hfuchs5

Copy Number Alteration Vignette

1

Added example heatmap under CNA_vignette **What changes are proposed in this pull request?** Added an example heatmap for copy number segmentation data **If there is an GitHub issue associated with...

alrein-05

Consider adding an additional merged version where fusions/cna/mutations are all separate side by side merged tables. Maybe we can come up with a prototype of this at the hackathon

2

karissawhiting

Improve documentation and color defaults for ggcomut

1

What is ggcomut measuring? Frequency? I.e. what do the numbers/colors mean? There are some white squares in the heatmap below – what do those mean compared to the tan? It’s...

hfuchs5

putting recoded cna character amp/del values into pivot_cna_wider() returns numeric values

1

cna % mutate(alteration = recode_cna(alteration)) View(cna) View(pivot_cna_wider(cna))

hfuchs5

1) Fusions Data - breakpointType - svStatus - variantClass - sometimes in fusions, site 1 is non impact gene but site 2 is impact gene (e.g. gnomeR::sv SHBG-TP53) - what...

karissawhiting