sigminer (version 1.0.5)

read_maf: Read MAF Files

Description

This function is a wrapper of maftools::read.maf. Currently, only mutation records used in signature identification and analysis. You can also use maftools::read.maf to read the data.

Usage

read_maf(
  maf,
  clinicalData = NULL,
  removeDuplicatedVariants = TRUE,
  useAll = TRUE,
  gisticAllLesionsFile = NULL,
  gisticAmpGenesFile = NULL,
  gisticDelGenesFile = NULL,
  gisticScoresFile = NULL,
  cnLevel = "all",
  cnTable = NULL,
  isTCGA = FALSE,
  vc_nonSyn = NULL,
  verbose = TRUE
)

Arguments

maf

tab delimited MAF file. File can also be gz compressed. Required. Alternatively, you can also provide already read MAF file as a dataframe.

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.

useAll

logical. Whether to use all variants irrespective of values in Mutation_Status. Defaults to TRUE. If FALSE, only uses with values Somatic.

gisticAllLesionsFile

All Lesions file generated by gistic. e.g; all_lesions.conf_XX.txt, where XX is the confidence level. Default NULL.

gisticAmpGenesFile

Amplification Genes file generated by gistic. e.g; amp_genes.conf_XX.txt, where XX is the confidence level. Default NULL.

gisticDelGenesFile

Deletion Genes file generated by gistic. e.g; del_genes.conf_XX.txt, where XX is the confidence level. Default NULL.

gisticScoresFile

scores.gistic file generated by gistic. Default NULL

cnLevel

level of CN changes to use. Can be 'all', 'deep' or 'shallow'. Default uses all i.e, genes with both 'shallow' or 'deep' CN changes

cnTable

Custom copynumber data if gistic results are not available. Input file or a data.frame should contain three columns in aforementioned order with gene name, Sample name and copy number status (either 'Amp' or 'Del'). Default NULL.

isTCGA

Is input MAF file from TCGA source. If TRUE uses only first 12 characters from Tumor_Sample_Barcode.

vc_nonSyn

NULL. Provide manual list of variant classifications to be considered as non-synonymous. Rest will be considered as silent variants. Default uses Variant Classifications with High/Moderate variant consequences. http://asia.ensembl.org/Help/Glossary?id=535: "Frame_Shift_Del", "Frame_Shift_Ins", "Splice_Site", "Translation_Start_Site","Nonsense_Mutation", "Nonstop_Mutation", "In_Frame_Del","In_Frame_Ins", "Missense_Mutation"

verbose

TRUE logical. Default to be talkative and prints summary.

See Also

read_copynumber for reading copy number data to CopyNumber object.

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools", mustWork = TRUE)
if (!require("R.utils")) {
  message("Please install 'R.utils' package firstly")
} else {
  laml <- read_maf(maf = laml.maf)
  laml
}
# }