% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllClasses.R, R/plageParam.R
\docType{class}
\name{plageParam-class}
\alias{plageParam-class}
\alias{plageParam}
\title{\code{plageParam} class}
\usage{
plageParam(
  exprData,
  geneSets,
  assay = NA_character_,
  annotation = NULL,
  minSize = 1,
  maxSize = Inf,
  verbose = TRUE
)
}
\arguments{
\item{exprData}{The expression data set.  Must be one of the classes
supported by \code{\linkS4class{GsvaExprData}}.  For a list of these classes, see its
help page using \code{help(GsvaExprData)}.}

\item{geneSets}{The gene sets.  Must be one of the classes supported by
\code{\linkS4class{GsvaGeneSets}}.  For a list of these classes, see its help page using
\code{help(GsvaGeneSets)}.}

\item{assay}{Character vector of length 1.  The name of the assay to use in
case \code{exprData} is a multi-assay container, otherwise ignored.  By default,
an assay called 'logcounts' will be used if present, otherwise the first
assay is used.}

\item{annotation}{An object of class \code{GeneIdentifierType} from
package \code{GSEABase} describing the gene identifiers used as the row names of
the expression data set.  See \code{GeneIdentifierType} for help on available
gene identifier types and how to construct them.  This
information can be used to map gene identifiers occurring in the gene sets.

If the default value \code{NULL} is provided, an attempt will be made to extract
the gene identifier type from the expression data set provided as \code{exprData}
(by calling \code{\link{gsvaAnnotation}} on it).  If still not successful, the
\code{NullIdentifier()} will be used as the gene identifier type, gene identifier
mapping will be disabled and gene identifiers used in expression data set and
gene sets can only be matched directly.}

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

\item{maxSize}{Numeric vector of length 1.  Maximum size of the resulting gene
sets after gene identifier mapping. By default, the maximum size is \code{Inf}.}

\item{verbose}{Logical vector of length 1. It gives information about some
decisions made by the software during parameter object construction when
\code{verbose=TRUE} (default) and remains silent otherwise.}
}
\value{
A new \code{\linkS4class{plageParam}} object.
}
\description{
S4 class for PLAGE method parameter objects.

Objects of class \code{plageParam} contain the parameters for running
the \code{PLAGE} method.
}
\details{
Since method PLAGE does not take any method-specific parameters, this
class does not add any slots to the common slots inherited from
\code{GsvaMethodParam}.

\code{PLAGE} takes a number of parameters shared with all methods
implemented by package GSVA but does not take any method-specific parameters.
These parameters are described in detail below.
}
\examples{
suppressPackageStartupMessages({
library(GSEABase)
library(GSVA)
library(GSVAdata)
})

data(geneprotExpCostaEtAl2021)
data(c2BroadSets)

## for simplicity, use only a subset of the sample data
se <- geneExpCostaEtAl2021[1:1000, ]
gsc <- c2BroadSets[1:100]
pp1 <- plageParam(se, gsc)
pp1

}
\references{
Tomfohr, J. et al. Pathway level analysis of gene expression
using singular value decomposition.
\emph{BMC Bioinformatics}, 6:225, 2005.
\doi{10.1186/1471-2105-6-225}
}
\seealso{
\code{\linkS4class{GsvaExprData}},
\code{\linkS4class{GsvaGeneSets}},
\code{\linkS4class{GsvaMethodParam}},
\code{\linkS4class{zscoreParam}},
\code{\linkS4class{ssgseaParam}},
\code{\linkS4class{gsvaParam}}

\code{\link[GSEABase:GeneIdentifierType-class]{GeneIdentifierType}}
}
