karissawhiting
karissawhiting
I noticed some inconsistencies between public cBioPortal and MSK cBioPortal regarding structural variant data. I'm also not able to pull structural variant data anymore via the API endpoint for these...
Included IMPACT genes differ depending on whether you pull panel ID `'MSK-IMPACT***'` or `'IMPACT***'` and also whether you are connected to public cBioPortal, internal MSK cBioPortal or internal GENIE cBioPortal....
See https://github.com/pcctc/croquet for inspo
- first check if our current ones are color blind friendly- @karissawhiting will find the tool that can help with this from mskRvis - If not, add a color blind...
Currently `subset_by_frequency()` will subset and only return alteration columns in your gene binary with > x% prevalence. Sometimes it's useful to calculate these frequency/inclusion cutoffs by keeping genes or alterations...
**What changes are proposed in this pull request?** **To-do's before merging** - [ ] Bring in any comments over from other PR and close that PR (https://github.com/MSKCC-Epi-Bio/gnomeR/pull/307). All code changes...
We can require this as a preprocessing step, or add an arg in `create_gene_binary()`. We will think on it more and maybe ask Caroline and Alli for preference. Maybe we...
@edrill suggested this. This can be useful for oncoprints and more in-depth mutation specific analyses. The relevant information seems to be in the following MAF columns: ``` r table(gnomeR::mutations$mutationType, gnomeR::mutations$variantType)...
```r library(dplyr) library(stringr) extract_patient_id % mutate(patient_id = str_replace(sample_id, "-T.*", ""))) } else { # If any value does not match the format, raise an error cli::cli_abort("Some {.code sample_id} values do...
Currently these are in the `inst` > `seg-stuff` folder. I removed some dependencies that these functions needed for now. We can add them back as needed ({iClusterPlus}, {GenomicRanges}, {lattice}, {iRanges},...