% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mnsea.R
\name{mnsea}
\alias{mnsea}
\title{Multi-layer Network-based Gene Set Enrichment Analysis}
\usage{
mnsea(
  seed_list,
  networks,
  couplings,
  gene_sets,
  mode = c("evidence", "signed"),
  layer_weights = NULL,
  collapse = c("weighted_mean", "sum", "mean", "max_abs"),
  target_layer = NULL,
  output_space = c("union", "gene"),
  p = 0.5,
  interlayer_strength = 1,
  specific_weight = FALSE,
  minGSSize = 10,
  maxGSSize = 500,
  threshold = 1e-09,
  maxIter = 100,
  verbose = TRUE,
  ...
)
}
\arguments{
\item{seed_list}{named list of named numeric vectors, one per layer.}

\item{networks}{named list of layer-specific networks.}

\item{couplings}{data.frame of inter-layer edges.}

\item{gene_sets}{list of gene sets.}

\item{mode}{one of "evidence" or "signed".}

\item{layer_weights}{optional named numeric vector.}

\item{collapse}{one of "weighted_mean", "sum", "mean", or "max_abs".}

\item{target_layer}{optional layer name to export scores from.}

\item{output_space}{one of "union" or "gene".}

\item{p}{restart probability.}

\item{interlayer_strength}{global scaling factor for coupling edges.}

\item{specific_weight}{logical.}

\item{minGSSize}{minimal size of each gene set.}

\item{maxGSSize}{maximal size of genes annotated for testing.}

\item{threshold}{convergence threshold.}

\item{maxIter}{maximal number of iterations.}

\item{verbose}{logical.}

\item{...}{additional arguments passed to \code{gsea()}.}
}
\value{
A \code{mnseaResult} object.
}
\description{
Multi-layer Network-based Gene Set Enrichment Analysis
}
