read_impact_repository_files: Helper functions to read files from MSK-IMPACT repository

read_impact_repository_filesR Documentation

Helper functions to read files from MSK-IMPACT repository

Description

Helper functions that reads the most commonly used filed from the MSK-IMPACT Mercurial repository.

Usage

read_impact_maf(filename = NULL, unfiltered = F, germline = F)

read_impact_cna(filename = NULL)

read_impact_fusions(filename = NULL)

read_impact_samples(filename = NULL)

read_impact_patients(filename = NULL)

Arguments

filename

Override default filenames, assumes they exist in default location

unfiltered

Read MAF containing non-signed out mutation calls

germline

Retain germline calls in MAF

Value

Data object in tweaked cBioPortal format


kpjonsson/kpjmisc documentation built on Jan. 14, 2024, 2:38 a.m.