Generates count matrix of mutations.
Generates a count matrix of mutations. i.e, number of mutations per gene per sample.
mutCountMatrix( maf, includeSyn = FALSE, countOnly = NULL, removeNonMutated = TRUE )
maf |
an MAF object generated by |
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 |
Integer Matrix
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')Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.