Read MAF Files

Source: R/read_maf.R

This function is a wrapper of maftools::read.maf. Useless options in maftools::read.maf are dropped here. You can also use maftools::read.maf to read the data. All reference alleles and mutation alleles should be recorded in positive strand format.

read_maf(maf, verbose = TRUE)

read_maf_minimal(dt)

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.

verbose

TRUE logical. Default to be talkative and prints summary.

dt

A data.frame contains at least the following columns: "Tumor_Sample_Barcode", "Chromosome", "Start_Position", "End_Position", "Reference_Allele", "Tumor_Seq_Allele2"

Functions

  • read_maf_minimal(): Read Maf data.frame from a minimal maf-like data

See also

read_copynumber for reading copy number data to CopyNumber object.

Examples

# \donttest{
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

  laml_mini <- laml@data[, list(
    Tumor_Sample_Barcode, Chromosome,
    Start_Position, End_Position,
    Reference_Allele, Tumor_Seq_Allele2
  )]
  laml2 <- read_maf_minimal(laml_mini)
  laml2
}
#> Loading required package: R.utils
#> Loading required package: R.oo
#> Loading required package: R.methodsS3
#> R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
#> R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help.
#> 
#> Attaching package: ‘R.oo’
#> The following object is masked from ‘package:R.methodsS3’:
#> 
#>     throw
#> The following objects are masked from ‘package:methods’:
#> 
#>     getClasses, getMethods
#> The following objects are masked from ‘package:base’:
#> 
#>     attach, detach, load, save
#> R.utils v2.12.3 (2023-11-18 01:00:02 UTC) successfully loaded. See ?R.utils for help.
#> 
#> Attaching package: ‘R.utils’
#> The following object is masked from ‘package:utils’:
#> 
#>     timestamp
#> The following objects are masked from ‘package:base’:
#> 
#>     cat, commandArgs, getOption, isOpen, nullfile, parse, warnings
#> -Reading
#> -Validating
#> -Silent variants: 475 
#> -Summarizing
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.214s elapsed (0.252s cpu) 
#> Please note that the generated MAF object is designed for mutational signature analysis, not recommended for Maftools analysis!
#> An object of class  MAF 
#>            ID summary  Mean Median
#>        <char>   <num> <num>  <num>
#> 1: NCBI_Build      NA    NA     NA
#> 2:     Center      NA    NA     NA
#> 3:    Samples     192    NA     NA
#> 4:     nGenes       1    NA     NA
#> 5:    Unknown    1732 9.021      9
#> 6:      total    1732 9.021      9
# }