\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{
}
\description{
This function builds an object of class
It contains the parameters that will be used by function
\code{\link{runAn}} to analyze the ICA decomposition
contained in an object of class
}
\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{