Retrieves information about cosmic variant IDs
getCosmicCounts(cosmic,
cosmicDirectory = "/wehisan/general/academic/grp_leukemia_genomics/data/resources/COSMIC",
onlyCensus = T, genome = "hg19")character: The cosmic IDs.
character: The directory where the cosmic files CosmicMutantExportCensus.tsv and CosmicMutantExport.tsv are located.
logical: Restrict to cosmic census genes.
For each cosmic ID, return whether it is seen in a census gene, and the mutations per million tumors (MPM) for that variant, as well as the average MPM over the gene (mutations per million tumors per basepair, MPMPB).