% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sigScore.R
\name{sigScore}
\alias{sigScore}
\title{Calculate Signature Score Using PCA, Mean, or Z-score Methods}
\usage{
sigScore(eset, methods = c("PCA", "mean", "zscore"))
}
\arguments{
\item{eset}{Normalized expression matrix with genes (signature) as rows and
samples as columns.}

\item{methods}{Scoring method: `"PCA"` (default) for principal component 1,
`"mean"` for mean expression, or `"zscore"` for z-score normalized mean.}
}
\value{
Numeric vector of length `ncol(eset)`; a score summarizing the rows
  of `eset`.
}
\description{
Computes signature scores from gene expression data using Principal
Component Analysis (PCA), mean-based, or z-score approaches.
}
\examples{
# Create small example expression matrix
set.seed(123)
test_eset <- matrix(rnorm(1000), nrow = 10, ncol = 100)
rownames(test_eset) <- paste0("Gene", 1:10)
colnames(test_eset) <- paste0("Sample", 1:100)

# Calculate scores
score_pca <- sigScore(eset = test_eset, methods = "PCA")
score_mean <- sigScore(eset = test_eset, methods = "mean")
score_zscore <- sigScore(eset = test_eset, methods = "zscore")
}
\author{
Dorothee Nickles, Dongqiang Zeng
}
