getCohortMutationMatrix: returns relevant mutations in samples in Genes of Interest

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

returns relevant mutations in samples in Genes of Interest

Description

returns relevant mutations in samples in Genes of Interest

Usage

getCohortMutationMatrix(
  GoI,
  Rdirectory,
  metaDataFile,
  excludeIndividuals = c(),
  excludeSamples = c(),
  GoIakas = c(),
  cpus = 1,
  includeGermlineLike = T
)

Arguments

GoI	character vector. Genes of interest for the analysis
Rdirectory	character The Rdirectory where the superFreq run was run.

Details

This function plots a mutation matrix showing CNAs and point mutations in the Genes of Interest across the analysed samples in the Rdirectory. Should be run after the superFreq() run has completed.

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