Subset MAF objects
Subsets MAF based on given conditions.
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" )
maf |
an MAF object generated by |
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 |
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 |
fields |
include only these fields along with necessary fields in the output |
mafObj |
returns output as MAF class |
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. |
subset table or an object of class MAF-class
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.