gnomeR (development version)

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() to allow retention of other clinical vars when using function 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

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

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.