% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/GSVA-pkg-deprecated.R, R/gsva.R
\name{GSVA-pkg-deprecated}
\alias{GSVA-pkg-deprecated}
\alias{gsva,HDF5Array,list-method}
\alias{gsva,SingleCellExperiment,GeneSetCollection-method}
\alias{gsva,SingleCellExperiment,list-method}
\alias{gsva,dgCMatrix,list-method}
\alias{gsva,SummarizedExperiment,GeneSetCollection-method}
\alias{gsva,SummarizedExperiment,list-method}
\alias{gsva,ExpressionSet,list-method}
\alias{gsva,ExpressionSet,GeneSetCollection-method}
\alias{gsva,matrix,GeneSetCollection-method}
\alias{gsva,matrix,list-method}
\title{Deprecated functions in package \code{GSVA}.}
\usage{
\S4method{gsva}{HDF5Array,list}(
  expr,
  gset.idx.list,
  annotation,
  method = c("gsva", "ssgsea", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson", "none"),
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  parallel.sz = 1L,
  mx.diff = TRUE,
  tau = switch(method, gsva = 1, ssgsea = 0.25, NA),
  ssgsea.norm = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(progressbar = verbose)
)

\S4method{gsva}{SingleCellExperiment,GeneSetCollection}(expr, gset.idx.list, ...)

\S4method{gsva}{SingleCellExperiment,list}(
  expr,
  gset.idx.list,
  annotation,
  method = c("gsva", "ssgsea", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson", "none"),
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  parallel.sz = 1L,
  mx.diff = TRUE,
  tau = switch(method, gsva = 1, ssgsea = 0.25, NA),
  ssgsea.norm = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(progressbar = verbose)
)

\S4method{gsva}{dgCMatrix,list}(
  expr,
  gset.idx.list,
  annotation,
  method = c("gsva", "ssgsea", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson", "none"),
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  parallel.sz = 1L,
  mx.diff = TRUE,
  tau = switch(method, gsva = 1, ssgsea = 0.25, NA),
  ssgsea.norm = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(progressbar = verbose)
)

\S4method{gsva}{SummarizedExperiment,GeneSetCollection}(
  expr,
  gset.idx.list,
  annotation,
  method = c("gsva", "ssgsea", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson", "none"),
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  parallel.sz = 1L,
  mx.diff = TRUE,
  tau = switch(method, gsva = 1, ssgsea = 0.25, NA),
  ssgsea.norm = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(progressbar = verbose)
)

\S4method{gsva}{SummarizedExperiment,list}(
  expr,
  gset.idx.list,
  annotation,
  method = c("gsva", "ssgsea", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson", "none"),
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  parallel.sz = 1L,
  mx.diff = TRUE,
  tau = switch(method, gsva = 1, ssgsea = 0.25, NA),
  ssgsea.norm = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(progressbar = verbose)
)

\S4method{gsva}{ExpressionSet,list}(
  expr,
  gset.idx.list,
  annotation,
  method = c("gsva", "ssgsea", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson", "none"),
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  parallel.sz = 1L,
  mx.diff = TRUE,
  tau = switch(method, gsva = 1, ssgsea = 0.25, NA),
  ssgsea.norm = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(progressbar = verbose)
)

\S4method{gsva}{ExpressionSet,GeneSetCollection}(
  expr,
  gset.idx.list,
  annotation,
  method = c("gsva", "ssgsea", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson", "none"),
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  parallel.sz = 1L,
  mx.diff = TRUE,
  tau = switch(method, gsva = 1, ssgsea = 0.25, NA),
  ssgsea.norm = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(progressbar = verbose)
)

\S4method{gsva}{matrix,GeneSetCollection}(
  expr,
  gset.idx.list,
  annotation,
  method = c("gsva", "ssgsea", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson", "none"),
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  parallel.sz = 1L,
  mx.diff = TRUE,
  tau = switch(method, gsva = 1, ssgsea = 0.25, NA),
  ssgsea.norm = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(progressbar = verbose)
)

\S4method{gsva}{matrix,list}(
  expr,
  gset.idx.list,
  annotation,
  method = c("gsva", "ssgsea", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson", "none"),
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  parallel.sz = 1L,
  mx.diff = TRUE,
  tau = switch(method, gsva = 1, ssgsea = 0.25, NA),
  ssgsea.norm = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(progressbar = verbose)
)
}
\description{
The functions listed below are deprecated and will be defunct in
the near future. When possible, alternative functions with similar
functionality are also mentioned. Help pages for deprecated functions are
available at \code{\link{gsva-deprecated}}.
}
\section{Details}{

Instead of gsva(expr=., gset.idx.list=., method=., ...), use a method-specific
parameter object,
see [\code{plageParam}][\code{zscoreParam}][\code{ssgseaParam}][\code{gsvaParam}],
followed by a call to the new \code{gsva()} function, see \code{\link{gsva}}.
}

\keyword{internal}
