subsetMaf: Subset MAF objects
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

subsetMaf

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,
  keepNA = FALSE,
  mult = "first",
  fields = NULL,
  mafObj = TRUE,
  includeSyn = TRUE,
  isTCGA = FALSE,
  dropLevels = TRUE,
  restrictTo = "all",
  verbose = TRUE
)

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'
`keepNA`	Keep NAs while sub-setting for ranges. Default 'FALSE' - removes rows with missing loci prior to overlapping. Set to TRUE to keep them as is.
`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.
`verbose`	Default TRUE

Value

subset table or an object of class MAF-class

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)

PoisonAlien/maftools documentation built on Nov. 5, 2024, 4:12 p.m.