mafCleanup: maf.cleanup

In bioinform/ecTMB: Esitmation and Classification of TMB

Description

maf.cleanup

Usage

mafCleanup(maf, extraCols = NULL, keepNoncoding = FALSE,
  save = FALSE, fn = "./output.tsv", nonSilTypes = NULL,
  SilTypes = NULL, ncTypes = NULL, gid = NULL)

Arguments

maf	Input maf file. It can be a path to either rda or tsv file or data.frame
extraCols	Default is NULL which no extra column will be included. If "all", all columns will be output. If an array, only specificed columns will be reported.
keepNoncoding	A boolen. If TRUE, the noncoding variants will be keeped. Default is FALSE, which noncoding variants will be removed.
save	A boolen. If TRUE, the file will be saved, FALSE, the file will not be saved
fn	string, the output file name
nonSilTypes	To specify what variant classification should be considered as nonsilent variants. Default is NULL which the default list of classification will be used.
SilTypes	To specify what variant classification should be considered as silent variants. Default is NULL which the default list of classification will be used.
ncTypes	To specify what variant classification should be considered as variants in noncoding regions. Default is NULL which the default list of classification will be used.
gid	Gene ID list.

Value

cleaned up maf file.

Examples

## Not run: 
maf.cleanup(x, output)

## End(Not run)

bioinform/ecTMB documentation built on Aug. 29, 2021, 6:17 p.m.