Creates a Genotype Matrix for every variant
Creates a Genotype matrix using allele frequcies or by muatation status.
genotypeMatrix( maf, genes = NULL, tsb = NULL, includeSyn = FALSE, vafCol = NULL, vafCutoff = c(0.1, 0.75) )
maf |
|
genes |
create matrix for only these genes. Define NULL |
tsb |
create matrix for only these tumor sample barcodes/samples. Define NULL |
includeSyn |
whether to include silent mutations. Default FALSE |
vafCol |
specify column name for vaf's. Default NULL. If not provided simply assumes all mutations are heterozygous. |
vafCutoff |
specify minimum and maximum vaf to define mutations as heterozygous. Default range 0.1 to 0.75. Mutations above maximum vafs are defined as homozygous. |
matrix
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
genotypeMatrix(maf = laml, genes = "RUNX1")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.