% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sex_interaction_analysis_bulk.R
\name{sex_interaction_analysis_bulk}
\alias{sex_interaction_analysis_bulk}
\title{Perform Sex-Phenotype Interaction Analysis for Bulk Data}
\usage{
sex_interaction_analysis_bulk(
  expression_data,
  phenotype,
  sex,
  phenotype_labels_vector = c("WT", "TG"),
  sex_labels_vector = c("F", "M"),
  min_logfc = 0.25,
  alpha = 0.05,
  min_samples = 20
)
}
\arguments{
\item{expression_data}{Numeric matrix of expression data (features x samples).}

\item{phenotype}{Character or factor vector of sample phenotypes.}

\item{sex}{Character or factor vector of sample sexes.}

\item{phenotype_labels_vector}{Character vector of phenotype levels (default c("WT","TG")).}

\item{sex_labels_vector}{Character vector of sex levels (default c("F","M")).}

\item{min_logfc}{Numeric. Minimum absolute log fold change for reporting significant genes (default 0.25).}

\item{alpha}{Numeric. FDR threshold for significance (default 0.05).}

\item{min_samples}{Integer. Minimum number of samples per group (default 20).}
}
\value{
A list with all DE results, filtered significant DEGs, and summary statistics.
}
\description{
Identifies genes whose expression is modulated by the interaction
between sex and phenotype using a differential difference contrast
}
