Generate gam from the maf file

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 as dataframe

sample.col

a list containing the elements to filter

gene.col

column in maf file to filter

value.var

column in maf file to filter

samples

column in maf file to filter

genes

column in maf file to filter

fun.aggregate

column in maf file to filter

binarize

a boolena to include or exclude the dataframe with values in list provided

fill

a grep argument to specify if grep use the argumnet as string or not

...

Other options

Value

filtered_maf a GAM matrix