man/nbOccInComp.Rd
14753e6b
 \name{nbOccInComp}
 \alias{nbOccInComp}
 \title{Select components the features contribute to}
 \usage{
   nbOccInComp(icaSet, params, selectionByComp = NULL,
     level = c("features", "genes"), file = NULL)
 }
 \arguments{
   \item{icaSet}{An object of class \code{\link{IcaSet}}}
 
   \item{params}{An object of class
   \code{\link{MineICAParams}} containing the parameters of
   the analysis, the attribute \code{cutoffSel} is used as a
   threshold on the absolute projections to determine which
   genes contribute to the components.}
 
   \item{selectionByComp}{The list of components already
   restricted to the contributing genes}
 
   \item{level}{The attribute of \code{icaSet} to be used,
   are reported the occurences of either the
   \code{"features"} or the \code{"genes"}.}
 
   \item{file}{The file where the output data.frame and
   plots are written.}
 }
 \value{
   Returns a data.frame whose columns are: 'gene' the
   feature or gene ID, 'nbOcc' the number of components on
   which the gene contributes according to the threshold,
   'components' the indices of these components, and then
   the component indices which contain its projection
   values.
 }
 \description{
   For each feature/gene, this function returns the
   components they contribute to and their projection values
   across all the components.
 }
 \details{
   A feature/gene is considered as a contributor when its
   scaled projection value exceeds the threshold
   \code{selCutoff(icaSet)}.
 
   This function plots the number of times the feature/gene
   is a contributor as a function of the standard deviation
   of its expression profile.
 
   The created files are located in \code{genePath(params)}.
   An extensiom '.htm' and '.pdf' is respectively added to
   the \code{file} name for the data.frame and the plot
   outputs.
 }
 \examples{
 data(icaSetCarbayo)
 params <- buildMineICAParams(resPath="carbayo/")
 nbOcc <- nbOccInComp(icaSet=icaSetCarbayo, params=params, level="genes", file="gene2MixingMatrix")
 }
 \author{
   Anne Biton
 }