% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllClasses.R, R/zscoreParam.R
\docType{class}
\name{zscoreParam-class}
\alias{zscoreParam-class}
\alias{zscoreParam}
\title{\code{zscoreParam} class}
\usage{
zscoreParam(
  exprData,
  geneSets,
  assay = NA_character_,
  annotation = NA_character_,
  minSize = 1,
  maxSize = Inf
)
}
\arguments{
\item{exprData}{The expression data.  Must be one of the classes
supported by \code{\linkS4class{GsvaExprData}}.}

\item{geneSets}{The gene sets.  Must be one of the classes supported by
\code{\linkS4class{GsvaGeneSets}}.}

\item{assay}{The name of the assay to use in case \code{exprData} is a multi-assay
container, otherwise ignored.  By default, the first assay is used.}

\item{annotation}{The name of a Bioconductor annotation package for the gene
identifiers occurring in the row names of the expression data matrix.  This
can be used to map gene identifiers occurring in the gene sets if those are
provided in a \code{\link{GeneSetCollection}}.  By default gene identifiers used in
expression data matrix and gene sets are matched directly.}

\item{minSize}{Minimum size of the resulting gene sets after gene identifier
mapping. By default, the minimum size is 1.}

\item{maxSize}{Maximum size of the resulting gene sets after gene identifier
mapping. By default, the maximum size is \code{Inf}.}
}
\value{
A new \code{\linkS4class{zscoreParam}} object.
}
\description{
Method-specific parameters for the combined z-scores method.

Objects of class \code{zscoreParam} contain the parameters for running
the combined z-scores method.
}
\details{
Since this method does not take any method-specific parameters, the parameter
class does not add any slots to the common slots inherited from
\code{\linkS4class{GsvaMethodParam}}.

The combined z-scores method does not take any method-specific
parameters in addition to an expression data set and a collection of gene
sets.
}
\examples{
library(GSVA)
library(GSVAdata)

data(leukemia)
data(c2BroadSets)

## for simplicity, use only a subset of the sample data
ses <- leukemia_eset[1:1000, ]
gsc <- c2BroadSets[1:100]
zp1 <- zscoreParam(ses, gsc)
zp1


}
\references{
Lee, E. et al. Inferring pathway activity toward precise
disease classification.
\emph{PLoS Comp Biol}, 4(11):e1000217, 2008.
\href{https://doi.org/10.1371/journal.pcbi.1000217}{DOI}
}
\seealso{
\code{\linkS4class{GsvaExprData}},
\code{\linkS4class{GsvaGeneSets}},
\code{\linkS4class{GsvaMethodParam}},
\code{\linkS4class{plageParam}},
\code{\linkS4class{ssgseaParam}},
\code{\linkS4class{gsvaParam}}
}
