\title{Tests association between qualitative variables and components.}
  qualVarAnalysis(params, icaSet, keepVar,
    keepComp = indComp(icaSet),
    keepSamples = sampleNames(icaSet),
    adjustBy = c("none", "component", "variable"),
    method = "BH", doPlot = TRUE, typePlot = "density",
    addPoints = FALSE, onlySign = TRUE,
    cutoff = params["pvalCutoff"],
    colours = annot2col(params), path = "qualVarAnalysis/",
    filename = "qualVar", typeImage = "png")
  \item{params}{An object of class
  providing the parameters of the analysis.}

  \item{icaSet}{An object of class

  \item{keepVar}{The variable labels to be considered, must
  be a subset of \code{varLabels(icaSet)}.}

  \item{keepComp}{A subset of components, must be included
  in \code{indComp(icaSet)}. By default, all components are

  \item{keepSamples}{A subset of samples, must be included
  in \code{sampleNames(icaSet)}. By default, all samples
  are used.}

  \item{adjustBy}{The way the p-values of the Wilcoxon and
  Kruskal-Wallis tests should be corrected for multiple
  testing: \code{"none"} if no p-value correction has to be
  done, \code{"component"} if the p-values have to be
  corrected by component, \code{"variable"} if the p-values
  have to be corrected by variable}

  \item{method}{The correction method, see
  \code{\link{p.adjust}} for details, default is
  \code{"BH"} for Benjamini & Hochberg.}

  \item{doPlot}{If TRUE (default), the plots are done, else
  only tests are performed.}

  \item{addPoints}{If TRUE, points are superimposed on the

  \item{typePlot}{The type of plot, either \code{"density"}
  or \code{"boxplot"}.}

  \item{onlySign}{If TRUE (default), only the significant
  results are plotted.}

  \item{cutoff}{A threshold p-value for statistical

  \item{colours}{A vector of colours indexed by the
  variable levels, if missing the colours are automatically
  generated using \code{\link{annot2Color}}.}

  \item{path}{A directory _within resPath(params)_ where
  the files containing the plots and the p-value results
  will be located. Default is \code{"qualVarAnalysis/"}.}

  \item{typeImage}{The type of image file to be used.}

  \item{filename}{The name of the HTML file containing the
  p-values of the tests, if NULL no file is created.}
  Returns A data.frame of dimensions 'components x
  variables' containing the p-values of the non-parametric
  tests (Wilcoxon or Kruskal-Wallis tests) wich test if the
  samples groups defined by each variable are differently
  distributed on the components.
  This function tests if the groups of samples formed by
  the variables are differently distributed on the
  components, in terms of contribution value (i.e of values
  in matrix \code{A(icaSet)}). The distribution of the
  samples on the components are represented using either
  density plots of boxplots. It is possible to restrict the
  tests and the plots to a subset of samples and/or
  This function writes an HTML file containing the results
  of the tests as a an array of dimensions 'variables *
  components' containing the p-values of the tests. When a
  p-value is considered as significant according to the
  threshold \code{cutoff}, it is written in bold and filled
  with a link pointing to the corresponding plot. One image
  is created by plot and located into the sub-directory
  "plots/" of \code{path}. Each image is named by
  index-of-component_var.png. Wilcoxon or Kruskal-Wallis
  tests are performed depending on the number of groups of
  interest in the considered variable (argument
## load an example of IcaSet

## build MineICAParams object
params <- buildMineICAParams(resPath="carbayo/")

## Define the directory containing the results
dir <- paste(resPath(params), "comp2annot/", sep="")

## Run tests, make no adjustment of the p-values,
# for variable grade and components 1 and 2,
# and plot boxplots when 'doPlot=TRUE'.
qualVarAnalysis(params=params, icaSet=icaSetCarbayo, adjustBy="none", typePlot="boxplot",
                keepVar="GRADE", keepComp=1:2, path=dir, doPlot=FALSE)
  Anne Biton
  , \code{\link{qualVarAnalysis}}, \code{\link{p.adjust}},
  \code{wilcox.test}, \code{kruskal.test}