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morinlab / GAMBLR.results

A collection of functions to access results of the Genomic Analysis of Mature B-cell Lymphomas
MIT License
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Add parameters to get_ssm_by_region(s) #53

Closed vladimirsouza closed 6 months ago

vladimirsouza commented 6 months ago

This PR addresses this issue.

get_ssm_by_regions behaviour is the same as before this PR. Bellow, I compare the output of get_ssm_by_regions before (maf_old_version) and after (maf_new_version) this PR.

### get maf tables
devtools::load_all("~/repos/gamblr_repos/GAMBLR.results")
maf_new_version = get_ssm_by_regions(regions_bed = GAMBLR.data::grch37_ashm_regions, 
                                     streamlined = F, basic_columns = T)

library(GAMBLR.results)
maf_old_version = get_ssm_by_regions(regions_bed = GAMBLR.data::grch37_ashm_regions, 
                                     streamlined = F, basic_columns = T)

> maf_new_version_na <- maf_new_version %>% replace(is.na(.), "NA")
> maf_old_version_na <- maf_old_version %>% replace(is.na(.), "NA")
> table(maf_new_version_na == maf_old_version_na)

   TRUE 
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