% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/selectX_stats.r
\name{interaction.table}
\alias{interaction.table}
\title{Build the full interaction results table from selectX outputs}
\usage{
interaction.table(
  al,
  als,
  obs,
  wobs,
  r.obs = NULL,
  r.wobs = NULL,
  null,
  maxFDR = 0.2,
  n.cores = 1,
  estimate_pairwise = FALSE,
  n.permut = 1000
)
}
\arguments{
\item{al}{Alteration landscape object (al$am, etc.)}

\item{als}{Alteration landscape stats (from al.stats)}

\item{obs}{Observed pairwise overlap matrix}

\item{wobs}{Weighted observed pairwise overlap matrix}

\item{r.obs}{List of null model overlap matrices}

\item{r.wobs}{List of null model weighted overlap matrices}

\item{null}{Null model list (simulated binary matrices)}

\item{maxFDR}{FDR cutoff for calling significant results}

\item{n.cores}{Number of cores}

\item{estimate_pairwise}{Whether to compute per-pair empirical p-values}

\item{n.permut}{Number of permutations}
}
\value{
Data frame with one row per gene pair and columns for overlap, effect sizes, FDR, and interaction type.
}
\description{
Build the full interaction results table from selectX outputs
}
\examples{
\donttest{
data(luad_run_data, package = "SelectSim")
result <- selectX(M = luad_run_data$M,
                  sample.class = luad_run_data$sample.class,
                  alteration.class = luad_run_data$alteration.class,
                  n.cores = 1, min.freq = 10, n.permut = 10,
                  verbose = FALSE)
head(result$result)
}

}
