karissawhiting
karissawhiting
Create a vignette in {gnomeR} to guide people through IMPACT data checks with explanations and examples - [ ] Decide what data set /samples to use. - [ ] Create...
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()`)....
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...
**What changes are proposed in this pull request?** Look up information by keywords **If there is an GitHub issue associated with this pull request, please provide link.** #39 -------------------------------------------------------------------------------- Reviewer...
Using environment file is no longer suggested. See https://happygitwithr.com/ and mskRutils vignettes
Previously examples used roxygen2's `@examplesIf` like: ``` r @examplesIf !httr::http_error("www.cbioportal.org/api") ``` However, when cBioPortal 5.0 came out, some of the underlying data used as example data sets were changed ("fusions"...
Currently you can't query by sample ID without also providing the study ID. Sometimes you may not know the study ID that a sample belongs to. We can potentially add...
Currently there isn't a designated API endpoint for pulling data by virtual study ID. One way you could do this is by pulling the session info. For example: ```r resp