\name{buildMineICAParams}
 \alias{buildMineICAParams}
 \title{Creates an object of class MineICAParams}
 \usage{
   buildMineICAParams(Sfile = new("character"),
     Afile = new("character"), datfile = new("character"),
     annotfile = new("character"), resPath = "", genesPath,
     annot2col = new("character"), pvalCutoff = 0.05,
     selCutoff = 3)
 }
 \arguments{
   \item{Sfile}{A txt file containing the Source matrix S.}
 
   \item{Afile}{A txt file containing the Mixing matrix A.}
 
   \item{datfile}{A txt file containing the data (e.g
   expression data) on which the decomposition was
   calculated.}
 
   \item{annotfile}{Either a "rda" or "txt" file containing
   the annotation data for the samples (must be of
   dimensions samples x annotations).}
 
   \item{resPath}{The path where the outputs of the analysis
   will be written, default is the current directory.}
 
   \item{genesPath}{The path _within_ the resPath where the
   gene projections will be written. If missing, will be
   automatically attributed as \code{resPath}/ProjByComp/.}
 
   \item{annot2col}{A vector of colors indexed by annotation
   levels. If missing, will be automatically attributed
   using function \code{annot2Color}.}
 
   \item{pvalCutoff}{The cutoff used to consider a p-value
   significant, default is 0.05.}
 
   \item{selCutoff}{The cutoff applied to the absolute
   feature/gene projection values to consider them as
   contributors, 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 a
   specific threshold is for each component.}
 }
 \value{
   An object of class \code{\link{MineICAParams}}
 }
 \description{
   This function builds an object of class
   \code{\link[MineICA:MineICAParams-class]{MineICAParams}}.
   It contains the parameters that will be used by function
   \code{\link{runAn}} to analyze the ICA decomposition
   contained in an object of class
   \code{\link[MineICA:IcaSet-class]{IcaSet}}.
 }
 \examples{
 ## define default parameters and fill resPath
 params <- buildMineICAParams(resPath="resMineICACarbayo/")
 
 ## change the default cutoff for selection of contribugint genes/features
 params <- buildMineICAParams(resPath="resMineICACarbayo/", selCutoff=4)
 }
 \author{
   Anne Biton
 }
 \seealso{
   \code{\link[MineICA:MineICAParams-class]{MineICAParams}},
   \code{\link[MineICA]{runAn}}
 }