Create an Alteration Landscape (AL) object

Builds an Alteration Landscape object from a list of genome alteration matrices and their corresponding tumor mutation burdens.

Usage

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

Arguments

am

A named list with two required elements: M (a named list of binary alteration matrices, each genes x samples) and tmb (a named list of data frames, one per matrix in M, each with columns sample and mutation). The names of M and tmb must match. All matrices in M must have identical row and column names.

feat.covariates

Named character vector of alteration-type annotations, one entry per feature (gene). Names must match rownames of the matrices in M. If NULL, all features are labelled "MUT".

sample.covariates

Named character vector of sample-type annotations, one entry per sample. Names must match colnames of the matrices in M. If NULL, all samples are labelled "sample".

min.freq

Minimum number of samples a gene must be mutated in (strictly greater than) to be retained. Features with rowSums <= min.freq are dropped.

verbose

Logical; print progress messages.

Value

An Alteration Landscape (AL) object (list of class "AL") containing the filtered alteration matrices, TMB vectors, and covariate assignments.

Examples

# \donttest{
data(luad_run_data, package = "SelectSim")
al <- new.AL.general(
  am               = luad_run_data$M,
  feat.covariates  = luad_run_data$alteration.class,
  sample.covariates = luad_run_data$sample.class,
  min.freq         = 10
)
# }