diff --git a/NEWS.md b/NEWS.md index 9fa4351a..c1ac4d92 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # gnomeR (development version) - +- More explicit separation between which are exported vs internal-only functions. +- Removed the sanitize_mutations(), sanitize_cna(), sanitize_fusions() functions and instead replaced them with smaller, more modular and explicit functions that do all the same tasks. (#328) - Added `extract_patient_id()` function to get IMPACT patient ID from sample ID - Deprecated `freq_cutoff`, `freq_cutoff_by_gene`, and `gene_subset` arguments in `tbl_genomic()`. It is now recommended that users use `subset_by_frequency()` instead before passing data to `tbl_genomic()`. - Added `other_vars` argument to `subset_by_frequency()`, `subset_by_panel()`, `summarize_by_gene()` and `add_pathways()` to allow retention of other clinical vars when using functions within pipeline. diff --git a/codemeta.json b/codemeta.json index 2c62b91e..01a94b1c 100644 --- a/codemeta.json +++ b/codemeta.json @@ -371,7 +371,7 @@ }, "SystemRequirements": null }, - "fileSize": "2349.143KB", + "fileSize": "2352.03KB", "releaseNotes": "https://github.com/MSKCC-Epi-Bio/gnomeR/blob/master/NEWS.md", "readme": "https://github.com/MSKCC-Epi-Bio/gnomeR/blob/main/README.md", "contIntegration": ["https://github.com/MSKCC-Epi-Bio/gnomeR/actions", "https://app.codecov.io/gh/MSKCC-Epi-Bio/gnomeR?branch=main"],