% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ImmuneSigR.R
\name{Score_ImmuneSigR}
\alias{Score_ImmuneSigR}
\alias{Score_CellSigR}
\title{Score Expression Data using ImmuneSigR}
\usage{
Score_ImmuneSigR(
  expr,
  target_cells = NULL,
  min_genes = 5,
  gmt_file = NULL,
  score_name = "_score",
  method = c("auto", "rank", "mean"),
  max_rank = 1500,
  verbose = TRUE,
  ...
)

Score_CellSigR(
  expr,
  target_cells = NULL,
  min_genes = 5,
  gmt_file = NULL,
  score_name = "_score",
  method = c("auto", "rank", "mean"),
  max_rank = 1500,
  verbose = TRUE,
  ...
)
}
\arguments{
\item{expr}{An expression matrix or data frame with genes in rows and cells in columns.}

\item{target_cells}{A character vector of target cell subpopulations to score. If NULL, scores all signatures.}

\item{min_genes}{Minimum number of genes required after filtering to genes present in the object.}

\item{gmt_file}{Optional path to a custom GMT file.}

\item{score_name}{Suffix used for generated score columns.}

\item{method}{Scoring method. "rank" is a dependency-free UCell-like rank score; "mean" uses average expression; "auto" uses "rank".}

\item{max_rank}{Maximum rank considered by the rank scoring method.}

\item{verbose}{Logical. If TRUE, prints progress messages.}

\item{...}{Reserved for future extensions.}
}
\value{
A data frame of scores with cells in rows and signatures in columns.
}
\description{
Scores expression matrices directly with dependency-free rank or mean methods.
}
\examples{
# Create a small toy expression matrix
set.seed(1)
toy_expr <- matrix(rpois(30, 2), nrow = 3,
                   dimnames = list(c("CD3D", "CD8A", "CD19"), paste0("cell_", 1:10)))
# Score the toy matrix (set min_genes = 2 because the toy matrix only has 3 genes)
scores <- Score_ImmuneSigR(toy_expr, target_cells = "T cell", min_genes = 2, method = "mean")
}
