% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils-accessors.R
\name{get_expr_matrix}
\alias{get_expr_matrix}
\title{Get Expression Matrix}
\usage{
get_expr_matrix(obj, type = "default", ...)
}
\arguments{
\item{obj}{A GseaEnv or GseaRes object.}

\item{type}{Character string specifying the type of expression values to return.
Options include: \code{"default"} (default display matrix), \code{"raw"}
(raw counts), \code{"cpm"} (counts per million), \code{"logcpm"}
(log2-transformed CPM), \code{"vst"} (variance stabilizing transformation,
DESeq2 only), \code{"fpkm"} (fragments per kilobase per million),
\code{"tpm"} (transcripts per million), and \code{"lognorm"} (log2 of
normalized counts).}

\item{...}{Additional arguments passed to backend-specific methods.}
}
\value{
A numeric matrix with genes as rows and samples as columns.
}
\description{
Extract expression matrix from GseaEnv or GseaRes object, supporting
  multiple normalization methods including raw counts, CPM, logCPM, VST, FPKM,
  TPM, and log-normalized counts.
}
\examples{
# Load pre-computed inputs shipped with the package
data(preprocessed_limma, package = "GSEAlens")

precomp <- preprocessed_limma
data(gsea_pathwaysets_toy, package = "GSEAlens")

pathways <- gsea_pathwaysets_toy
gsea_env <- setup_gsea_env(
  fit = precomp$fit,
  pathway_obj = pathways,
  expr_data = precomp$gsea_limma_voom_data
)
expr <- get_expr_matrix(gsea_env)
dim(expr)
}
