getCosmicCounts: Retrieves information about cosmic variant IDs

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

Retrieves information about cosmic variant IDs

Description

Retrieves information about cosmic variant IDs

Usage

getCosmicCounts(
  cosmic,
  cosmicDirectory =
    "/wehisan/general/academic/grp_leukemia_genomics/data/resources/COSMIC",
  onlyCensus = T,
  genome = "hg19"
)

Arguments

cosmic	character: The cosmic IDs.
cosmicDirectory	character: The directory where the cosmic files CosmicMutantExportCensus.tsv and CosmicMutantExport.tsv are located.
onlyCensus	logical: Restrict to cosmic census genes.

Details

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).

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.