% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/selectX_create.r
\name{new.AL.general}
\alias{new.AL.general}
\title{Create an Alteration Landscape (AL) object}
\usage{
new.AL.general(
  am,
  feat.covariates = NULL,
  sample.covariates = NULL,
  min.freq,
  verbose = FALSE
)
}
\arguments{
\item{am}{A named list with two required elements: \code{M} (a named list of binary
alteration matrices, each genes x samples) and \code{tmb} (a named list of data
frames, one per matrix in \code{M}, each with columns \code{sample} and
\code{mutation}). The names of \code{M} and \code{tmb} must match. All matrices
in \code{M} must have identical row and column names.}

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

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

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

\item{verbose}{Logical; print progress messages.}
}
\value{
An Alteration Landscape (AL) object (list of class \code{"AL"}) containing
the filtered alteration matrices, TMB vectors, and covariate assignments.
}
\description{
Builds an Alteration Landscape object from a list of genome alteration matrices
and their corresponding tumor mutation burdens.
}
\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
)
}

}
