cbioportalR

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How to get mRNA expression profiles

2

Dear @karissawhiting , I am opening another issue as I have been unable to load mRNA expression profiles from cbioportal. I tried the following. ``` set_cbioportal_db("public") mycancerstudy

ypradat

**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...

karissawhiting

Update README to Also Suggest Using {keyring} to Hold cBioPortal Authentication Info

2

Using environment file is no longer suggested. See https://happygitwithr.com/ and mskRutils vignettes

karissawhiting

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"...

karissawhiting

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...

karissawhiting

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

karissawhiting