Create an AL object

Create an Alteration Landscape (AL) object which contains gams and mutation burden of samples of associated gams.

Usage

new.AL.general(
  am,
  feat.covariates = NULL,
  sample.covariates = NULL,
  min.freq,
  verbose = FALSE
)

Arguments

am

The binary alteration matrix with row as features and column as samples.

feat.covariates

gene/feature covariate.

sample.covariates

sample covariate.

min.freq

minimum frequency of genes to be mutated.

verbose

print the time and each steps.

Value

An Alteration Landscape (AL) object with the gam.