\name{MineICAParams}
 \docType{class}
 \alias{class:MineICAParams}
 \alias{MineICAParams}
 \alias{MineICAParams-class}
 \alias{Sfile}
 \alias{getSfile}
 \alias{setSfile}
 \alias{Sfile<-}
 \alias{Sfile,MineICAParams-method}
 \alias{Sfile<-,MineICAParams,character-method}
 \alias{datfile}
 \alias{getdatfile}
 \alias{setdatfile}
 \alias{datfile<-}
 \alias{annotfile<-,MineICAParams-method}
 \alias{genesPath<-,ANY-method}
 \alias{resPath<-,ANY-method}
 \alias{selCutoff<-,MineICAParams-method}
 \alias{pvalCutoff<-,MineICAParams-method}
 \alias{Afile<-,MineICAParams-method}
 \alias{Sfile<-,MineICAParams-method}
 \alias{annot2col<-,MineICAParams-method}
 \alias{datfile<-,MineICAParams-method}
 \alias{datfile,MineICAParams-method}
 \alias{datfile<-,MineICAParams,character-method}
 \alias{Afile}
 \alias{getAfile}
 \alias{setAfile}
 \alias{Afile<-}
 \alias{Afile,MineICAParams-method}
 \alias{Afile<-,MineICAParams,character-method}
 \alias{annotfile}
 \alias{getAnnotfile}
 \alias{setAnnotfile}
 \alias{annotfile<-}
 \alias{annotfile,MineICAParams-method}
 \alias{annotfile<-,MineICAParams,character-method}
 \alias{resPath}
 \alias{getResPath}
 \alias{setResPath}
 \alias{resPath<-}
 \alias{resPath,MineICAParams-method}
 \alias{resPath<-,MineICAParams,character-method}
 \alias{genesPath}
 \alias{getGenesPath}
 \alias{setGenesPath}
 \alias{genesPath<-}
 \alias{genesPath,MineICAParams-method}
 \alias{genesPath<-,MineICAParams,character-method}
 \alias{annot2col}
 \alias{getAnnot2col}
 \alias{setAnnot2col}
 \alias{annot2col<-}
 \alias{annot2col,MineICAParams-method}
 \alias{annot2col<-,MineICAParams,character-method}
 \alias{pvalCutoff}
 \alias{getPvalCutoff}
 \alias{setPvalCutoff}
 \alias{pvalCutoff<-}
 \alias{pvalCutoff,MineICAParams-method}
 \alias{pvalCutoff<-,MineICAParams,numeric-method}
 \alias{selCutoff}
 \alias{getSelCutoff}
 \alias{setSelCutoff}
 \alias{selCutoff<-}
 \alias{selCutoff,MineICAParams-method}
 \alias{selCutoff<-,MineICAParams,numeric-method}
 
 %\alias{[}
 \alias{[,ANY,MineICAParams-method} 
 \alias{[,ANY,ANY,MineICAParams-method}
 \alias{[,ANY,ANY,ANY,MineICAParams-method}
 \alias{[,MineICAParams,ANY-method} 
 \alias{[,MineICAParams,ANY,ANY-method} 
 \alias{[,MineICAParams,ANY,ANY,ANY-method} 
 %\alias{[<-}
 \alias{[<-,MineICAParams,ANY,ANY,ANY,ANY-method} 
 \alias{[<-,MineICAParams,ANY,ANY,ANY-method} 
 \alias{[<-,MineICAParams,ANY,ANY-method} 
 %\alias{[<-,MineICAparams,ANY-method} 
 
 
 \title{
   Class to contain parameters for the analysis of an ICA decomposition.
 }
 
 \description{
   Container for parameters used during the analysis of an ICA
   decomposition obtained on genomics data.
 }
 \section{Creating Objects}{
 
   \code{new("MineICAParams")}
 
   \code{new("MineICAParams",
     resPath="",
     genesPath="ProjByComp",
     pvalCutoff=0.05,
     selCutoff=3)
   }
 }
 
 \section{Slots}{
   \describe{
 \item{\code{Sfile}}{ A txt file containing the Source matrix S.} 
 \item{\code{Afile}}{ A txt file containing the Mixing matrix A.} 
 \item{\code{datfile}}{ A txt file containing the data (typically expression data) on which the decomposition was calculated.}
 \item{\code{annotfile}}{ Either a RData or txt file containing the annotation data for the samples (must be of dimensions samples*annotations).} 
 \item{\code{resPath}}{ The path where the outputs of the analysis will be written.} 
 \item{\code{genesPath}}{ The path _within_ the resPath where the gene projections will be written. If missing, will be automatically attributed as resPath/gene2components/.}
 \item{\code{annot2col}}{ A vector of colors indexed by annotation levels. If missing, will be automatically attributed using function \code{annot2Color}.}
 \item{\code{pvalCutoff}}{ The cutoff used to consider a p-value significant, default is 0.05.}
 \item{\code{selCutoff}}{ The cutoff applied on the absolute feature/gene
   projection values to consider gene as contributing to a component,
   default is 3. Must be either of length 1 and the same treshold is
   applied to all components, or of length equal to the number of
   components in order to use a specific threshold for each component.} 
   }
   
 }
 \section{Methods}{
   \describe{
      For any slot:
      \item{\code{slotName(MineICAParams)} and
        \code{slotName(MineICAParams)<-}:}{Accessing and setting any slot
        of name \code{slotName} contained in an MineICAParams object.}   
       \item{\code{MineICAParams["slotName"]} and
 	\code{MineICAParams["slotName"]<-}:}{Accessing and setting any
 	slot of name \code{slotName} contained in an MineICAParams object.}   
    }
 }
    
 
   
 
 
 
 \author{Anne Biton}
 
 \seealso{
   \code{\link{MineICAParams-class}}, \code{\link{runAn}}.
 }
 
 \examples{
 # create an instance of LocSet
 new("MineICAParams")
 
 
 }
 
 \keyword{classes}