icgcSimpleMutationToMAF: Converts ICGC Simple Somatic Mutation format file to MAF

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Converts ICGC Simple Somatic Mutation format file to Mutation Annotation Format. Basic fields are converted as per MAF specififcations, rest of the fields are retained as in the input file. Ensemble gene IDs are converted to HGNC Symbols. Note that by default Simple Somatic Mutation format contains all affected transcripts of a variant resuting in multiple entries of the same variant in same sample. It is hard to choose a single affected transcript based on annotations alone and by default this program removes repeated variants as duplicated entries. If you wish to keep all of them, set removeDuplicatedVariants to FALSE.

Usage

icgcSimpleMutationToMAF(
  icgc,
  basename = NA,
  MAFobj = FALSE,
  clinicalData = NULL,
  removeDuplicatedVariants = TRUE,
  addHugoSymbol = FALSE
)

Arguments

icgc	Input data in ICGC Simple Somatic Mutation format. Can be gz compressed.
basename	If given writes to output file with basename.
MAFobj	If TRUE returns results as an MAF object.
clinicalData	Clinical data associated with each sample/Tumor_Sample_Barcode in MAF. Could be a text file or a data.frame. Default NULL.
removeDuplicatedVariants	removes repeated variants in a particuar sample, mapped to multiple transcripts of same Gene. See Description. Default TRUE.
addHugoSymbol	If TRUE replaces ensemble gene IDs with Hugo_Symbols. Default FALSE.

Details

ICGC Simple Somatic Mutattion format specififcation can be found here: http://docs.icgc.org/submission/guide/icgc-simple-somatic-mutation-format/

Value

tab delimited MAF file.

Examples

esca.icgc <- system.file("extdata", "simple_somatic_mutation.open.ESCA-CN.sample.tsv.gz", package = "maftools")
esca.maf <- icgcSimpleMutationToMAF(icgc = esca.icgc)

Example output

--Removed 427 duplicated variants

maftools documentation built on Feb. 6, 2021, 2 a.m.