% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/multi_omics.R
\name{aggregate_omics}
\alias{aggregate_omics}
\title{Aggregate multi-omics gene/protein-level statistics}
\usage{
aggregate_omics(
  x,
  method = c("fisher", "stouffer", "brown", "mean", "weighted_mean", "max_abs"),
  input = c("pvalue", "signed_score"),
  feature_type = "gene",
  conflict_policy = c("keep_all", "strict", "penalty"),
  ...
)
}
\arguments{
\item{x}{A list of named numeric vectors, a data.frame, or a matrix. Row names (or names for vectors) must represent feature IDs.}

\item{method}{Character, aggregation method. One of "fisher", "stouffer", "mean", or "max_abs".}

\item{input}{Character, input type. One of "pvalue" or "signed_score".}

\item{feature_type}{Character, type of the features (e.g., "gene", "protein"). Default is "gene".}

\item{conflict_policy}{Character, strategy to handle directional conflicts when input is "signed_score". One of "keep_all" (default, ignore conflicts), "strict" (set to NA if any signs conflict), or "penalty" (divide final score by 2 if signs conflict).}

\item{...}{Additional arguments.}
}
\value{
An object of class \code{omics_aggregated} containing \code{score}, \code{pvalue} (if input is "pvalue"), \code{input_type}, \code{feature_type}, and \code{feature_id}.
}
\description{
Aggregate multi-omics or multi-source statistics into a unified object for downstream enrichment analysis.
}
