mutCountMatrix: Generates count matrix of mutations.

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

Generates count matrix of mutations.

Description

Generates a count matrix of mutations. i.e, number of mutations per gene per sample.

Usage

mutCountMatrix(
  maf,
  includeSyn = FALSE,
  countOnly = NULL,
  removeNonMutated = TRUE
)

Arguments

maf	an MAF object generated by read.maf
includeSyn	whether to include sysnonymous variants in ouput matrix. Default FALSE
countOnly	Default NULL - counts all variants. You can specify type of 'Variant_Classification' to count. For e.g, countOnly = 'Splice_Site' will generates matrix for only Splice_Site variants.
removeNonMutated	Logical Default TRUE, removes samples with no mutations from the matrix.

Value

Integer Matrix

See Also

getFields getGeneSummary getSampleSummary

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
##Generate matrix
mutCountMatrix(maf = laml)
##Generate count matrix of Splice_Site mutations
mutCountMatrix(maf = laml, countOnly = 'Splice_Site')

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