subsetMaf {maftools} | R Documentation

## Subset MAF objects

### Description

Subsets MAF based on given conditions.

### Usage

    subsetMaf(
      maf,
      tsb = NULL,
      genes = NULL,
      query = NULL,
      clinQuery = NULL,
      ranges = NULL,
      mult = "first",
      fields = NULL,
      mafObj = TRUE,
      includeSyn = TRUE,
      isTCGA = FALSE,
      dropLevels = TRUE,
      restrictTo = "all"
    )

### Arguments

`maf` | an MAF object generated by `read.maf`
`tsb` | subset by these samples (Tumor Sample Barcodes)
`genes` | subset by these genes
`query` | query string. e.g, "Variant_Classification == 'Missense_Mutation'" returns only Missense variants.
`clinQuery` | query by clinical variable.
`ranges` | subset by ranges. data.frame with 3 column (chr, start, end). Overlaps are identified by `foverlaps` function with arguments 'type = within', 'mult = all', 'nomatch = NULL'
`mult` | When multiple loci in 'ranges' match to the variants maf, mult=. controls which values are returned - "all" , "first" (default) or "last". This value is passed to 'mult' argument of `foverlaps`
`fields` | include only these fields along with necessary fields in the output
`mafObj` | returns output as MAF class `MAF-class`. Default TRUE
`includeSyn` | Default TRUE, only applicable when mafObj = FALSE. If mafObj = TRUE, synonymous variants will be stored in a seperate slot of MAF object.
`isTCGA` | Is input MAF file from TCGA source.
`dropLevels` | Default TRUE.
`restrictTo` | restrict subset operations to these. Can be 'all', 'cnv', or 'mutations'. Default 'all'. If 'cnv' or 'mutations', subset operations will only be applied on copy-number or mutation data respectively, while retaining other parts as is.

### Value

subset table or an object of class `MAF-class`

### See Also

`getFields`

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    ##Select all Splice_Site mutations from DNMT3A and NPM1
    subsetMaf(maf = laml, genes = c('DNMT3A', 'NPM1'),
    query = "Variant_Classification == 'Splice_Site'")
    ##Select all variants with VAF above 30%
    subsetMaf(maf = laml, query = "i_TumorVAF_WU > 30")
    ##Extract data for samples 'TCGA.AB.3009' and 'TCGA.AB.2933' but only include vaf filed.
    subsetMaf(maf = laml, tsb = c('TCGA-AB-3009', 'TCGA-AB-2933'), fields = 'i_TumorVAF_WU')
    ##Subset by ranges
    ranges = data.frame(chr = c("2", "17"), start = c(25457000, 7571720), end = c(25458000, 7590868))
    subsetMaf(laml, ranges = ranges)

[Package maftools version 2.10.05 Index]