NEWS.md
In MSKCC-Epi-Bio/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

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.
Deprecated count_pathways_by argument of add_pathways() function. Now, user must specify which specific alteration to count towards the pathway via the .mut, .Amp, .Del, .fus suffix (e.g. custom_pathways = c('TP53.mut', 'APC.Del)).
Added IMPACT QA Vignette and GENIE BPC vignette
Added subset_by_panel function allowing users to easily subset an alteration dataframe and include only genes in a specific panel
Added IMPACT IH3 and IH4 panels to internal impact panels used for NA annotation in create_gene_binary(specify_panel)
Added GENIE BPC alias table so users can now use create_gene_binary(recode_aliases = "genie") to check and recode aliases for genes in any of the GENIE BPC panels.
Fixed bug in add_pathways() where custom_pathways wasn't catching all types of alterations when GENE.all was used due to paste0() vectorization.
Changed some arguments to strict matching (rlang::arg_match()) instead of partial matching (match.arg()) (e.g. mut_type = "s" doesn't work anymore and must be fully specified mut_type = "somatic_only").
Added unit tests for gnomeR plots/visuals (#144).
A dictionary of old to new names for rename_columns() output is now an attribute of the returned object. Now messages can reference the original names of data columns (ex: TumorAllele2 not tumor_allele_2) to make it more intuitive to users (#302).
Fixed bug that wasn't consistently filtering out germline samples
Enhanced subset_by_frequency() to users to select hugo_symbols if they reach a threshold in any level of a variable (ex: high risk vs low risk) (#305)

gnomeR 1.2.0

Updated color palette functionality
Column with sample ID now returned in data frame resulting from create_gene_binary()
summarize_by_gene() function was changed to run faster (#259)
subset_by_frequency() added to allow users to filter for specific prevalence levels of mutations/alterations/fusions (#270)
Removed oncoKB functionality (moving to {oncokbR} package)
Fixed bugs in tbl_genomic() and create_gene_binary().
Added data processing tutorial vignette

gnomeR 1.1.1

Package overhauled including main binary matrix functions. This is a pre-v2 release made because internal workshop was taught using this version of functions. Final/stable versions of these functions will be available in v2.0.0.