subsetMaf: Subset MAF objects

In maftools: Summarize, Analyze and Visualize MAF Files

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)

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