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Generate gam from the maf file

Source: R/gam_utils.r
maf2gam.Rd

maf2gam() takes a maf file and converts into gam

Usage

maf2gam(
  maf,
  sample.col = "Tumor_Sample_Barcode",
  gene.col = "Hugo_Symbol",
  value.var = "HGVSp_Short",
  samples = NULL,
  genes = NULL,
  fun.aggregate = length,
  binarize = TRUE,
  fill = NA
)

Arguments

maf

A MAF dataframe

sample.col

Column name for sample IDs

gene.col

Column name for gene symbols

value.var

Column used as the value to aggregate

samples

Vector of sample IDs to include; NULL keeps all samples present in the MAF

genes

Vector of gene names to include; NULL keeps all genes present in the MAF

fun.aggregate

Aggregation function applied per (sample, gene) cell

binarize

If TRUE, convert aggregated counts to binary presence/absence

fill

Value used for missing (sample, gene) combinations

Value

Numeric matrix (samples x genes) representing the gene alteration matrix.

Examples

data(luad_maf, package = "SelectSim")
gam <- maf2gam(luad_maf)
dim(gam)
#> [1]   502 18707