subsetMaf: Subset MAF objects

View source: R/subsetMaf.R

subsetMafR 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)


PoisonAlien/maftools documentation built on March 26, 2024, 11:13 a.m.