\name{buildIcaSet}
 \alias{buildIcaSet}
 \title{This function builds an object of class \code{\link{IcaSet}}.}
 \usage{
   buildIcaSet(params, A, S, dat, pData = new("data.frame"),
     fData = new("data.frame"), witGenes = new("character"),
     compNames = new("character"),
     refSamples = new("character"),
     annotation = new("character"),
     chipManu = new("character"),
     chipVersion = new("character"), alreadyAnnot = FALSE,
     typeID = c(geneID_annotation = "SYMBOL", geneID_biomart = "hgnc_symbol", featureID_biomart = ""),
     runAnnot = TRUE, organism = "Human",
     mart = new("Mart"))
 }
 \arguments{
   \item{params}{An object of class
   \code{\link{MineICAParams}} containing the parameters of
   the analysis}
 
   \item{A}{The mixing matrix of the ICA decomposition (of
   dimension samples x components).}
 
   \item{S}{The source matrix of the ICA decomposition (of
   dimension features x components).}
 
   \item{dat}{The data matrix the ICA was applied to (of
   dimension features x samples).}
 
   \item{pData}{Phenotype data, a data.frame which contains
   the sample informations of dimension samples x
   annotations.}
 
   \item{fData}{Feature data, a data.frame which contrains
   the feature descriptions of dimensions features x
   annotations.}
 
   \item{witGenes}{A vector of witness genes. They are
   representative of the expression behavior of the
   contributing genes of each component. If missing or NULL,
   they will be automatically attributed using function
   \code{\link{selectWitnessGenes}}.}
 
   \item{compNames}{A vector of component labels.}
 
   \item{refSamples}{A vector of reference sample IDs (e.g
   the "normal" samples).}
 
   \item{annotation}{An annotation package (e.g a ".db"
   package specific to the microarray used to generate
   \code{dat})}
 
   \item{chipManu}{If microarray data, the manufacturer:
   either 'affymetrix' or 'illumina'.}
 
   \item{chipVersion}{For illumina microarrays: the version
   of the microarray.}
 
   \item{alreadyAnnot}{TRUE if the feature IDs contained in
   the row names of \code{dat} and \code{S} already
   correspond to the final level of annotation (e.g if they
   are already gene IDs). In that case, no annotation is
   performed.}
 
   \item{typeID}{A character vector specifying the
   annotation IDs, it includes three elements : \describe{
   \item{geneID_annotation}{the IDs from the package to be
   used to annotate the features into genes. It will be used
   to fill the attributes \code{datByGene} and
   \code{SByGene} of the \code{icaSet}. It must match one of
   the objects the corresponding package supports (you can
   access the list of objects by typing
   ls("package:packagename")). If no annotation package is
   provided, this element is not useful.}
   \item{geneID_biomart}{the type of gene IDs, as available
   in \code{listFilters(mart)}; where mart is specified as
   described in \code{\link[biomaRt]{useMart}}. If you have
   directly built the IcaSet at the gene level (i.e if no
   annotation package is used), \code{featureID_biomart} and
   \code{geneID_biomart} will be identical.}
   \item{featureID_biomart}{the type of feature IDs, as
   available in \code{listFilters(mart)}; where \code{mart}
   is specified as described in function
   \code{\link[biomaRt]{useMart}}. Not useful if you work at
   the gene level.} }}
 
   \item{runAnnot}{If TRUE, \code{icaSet} is annotated with
   function \code{annotInGene}.}
 
   \item{organism}{The organism the data correspond to.}
 
   \item{mart}{The mart object (database and dataset) used
   for annotation, see function \code{useMart} of package
   \code{biomaRt}}
 }
 \value{
   An object of class IcaSet
 }
 \description{
   This function builds an object of class
   \code{\link{IcaSet}}.
 }
 \examples{
 dat <- data.frame(matrix(rnorm(10000),ncol=10,nrow=1000))
 rownames(dat) <- paste("g", 1:1000, sep="")
 colnames(dat) <- paste("s", 1:10, sep="")
 
 ## build a data.frame containing sample annotations
 annot <- data.frame(type=c(rep("a",5),rep("b",5)))
 rownames(annot) <- colnames(dat)
 
 ## run ICA
 resJade <- runICA(X=dat, nbComp=3, method = "JADE")
 
 ## build params
 params <- buildMineICAParams(resPath="toy/")
 
 ## build IcaSet object
 icaSettoy <- buildIcaSet(params=params, A=data.frame(resJade$A), S=data.frame(resJade$S),
                          dat=dat, pData=annot, alreadyAnnot=TRUE)
 params <- icaSettoy$params
 icaSettoy <- icaSettoy$icaSet
 
 \dontrun{
 ## load data
 library(breastCancerMAINZ)
 data(mainz)
 
 ## run ICA
 resJade <- runICA(X=dataMainz, nbComp=10, method = "JADE", maxit=10000)
 
 ## build params
 params <- buildMineICAParams(resPath="mainz/")
 
 ## build IcaSet object
 
 # fill typeID, Mainz data originate from affymetrix HG-U133a  microarray and are indexed by probe sets
 # we want to annotate the probe sets into Gene Symbols
 typeIDmainz <-  c(geneID_annotation="SYMBOL", geneID_biomart="hgnc_symbol", featureID_biomart="affy_hg_u133a")
 
 icaSetMainz <- buildIcaSet(params=params, A=data.frame(resJade$A), S=data.frame(resJade$S),
                              dat=exprs(mainz), pData=pData(mainz),
                              annotation="hgu133a.db", typeID= c(geneID_annotation = "SYMBOL",
                              geneID_biomart = "hgnc_symbol", featureID_biomart = "affy_hg_u133a"),
                              chipManu = "affymetrix", runAnnot=TRUE,
                              mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl"))
 }
 }
 \author{
   Anne Biton
 }
 \seealso{
   \code{\link{selectWitnessGenes}},
   \code{\link{annotInGene}}
 }