- Deprecated
freq_cutoff
,freq_cutoff_by_gene
, andgene_subset
arguments intbl_genomic()
. It is now recommended that users usesubset_by_frequency()
instead before passing data totbl_genomic()
. - Added
other_vars
argument tosubset_by_frequency()
to allow retention of other clinical vars when using function within pipeline. - Deprecated
count_pathways_by
argument ofadd_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
- 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()
andcreate_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.
- Major changes to come. For code written pre 3/23/2022 use this release
- Added a
NEWS.md
file to track changes to the package.