read.maf: Read MAF files.

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Takes tab delimited MAF (can be plain text or gz compressed) file as an input and summarizes it in various ways. Also creates oncomatrix - helpful for visualization.

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.

Details

This function takes MAF file as input and summarizes them. If copy number data is available, e.g from GISTIC, it can be provided too via arguments gisticAllLesionsFile, gisticAmpGenesFile, and gisticDelGenesFile. Copy number data can also be provided as a custom table containing Gene name, Sample name and Copy Number status.

Note that if input MAF file contains multiple affected transcripts of a variant, this function by default removes them as duplicates, while keeping single unique entry per variant per sample. If you wish to keep all of them, set removeDuplicatedVariants to FALSE.

FLAGS - If you get a note on possible FLAGS while reading MAF, it means some of the top mutated genes are fishy. These genes are often non-pathogenic and passengers, but are frequently mutated in most of the public exome studies. Examples of such genes include TTN, MUC16, etc. This note can be ignored without any harm, it's only generated as to make user aware of such genes. See references for details on FLAGS.

Value

An object of class MAF.

References

Shyr C, Tarailo-Graovac M, Gottlieb M, Lee JJ, van Karnebeek C, Wasserman WW. FLAGS, frequently mutated genes in public exomes. BMC Med Genomics 2014; 7: 64.

See Also

plotmafSummary write.mafSummary

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.544s elapsed (0.490s cpu) 

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