Anne Biton authored on 23/04/2020 18:30:14
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} |
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\arguments{
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\item{params}{An object of class
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- \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
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+ \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
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providing the parameters of the analysis.} |
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\item{icaSet}{An object of class
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- \code{\link[MineICA:IcaSet-class]{IcaSet}}.}
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+ \code{\link[MineICA:class-IcaSet]{IcaSet}}.}
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\item{keepVar}{The variable labels to be considered, must
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be a subset of \code{varLabels(icaSet)}.}
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@73179 bc3139a8-67e5-0310-9ffc-ced21a209358
Marc Carlson authored on 05/02/2013 22:15:53
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new file mode 100644 |
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+\name{qualVarAnalysis}
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+\alias{qualVarAnalysis}
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+\title{Tests association between qualitative variables and components.}
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+\usage{
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+ qualVarAnalysis(params, icaSet, keepVar, |
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+ keepComp = indComp(icaSet), |
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+ keepSamples = sampleNames(icaSet), |
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+ adjustBy = c("none", "component", "variable"),
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+ method = "BH", doPlot = TRUE, typePlot = "density", |
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+ addPoints = FALSE, onlySign = TRUE, |
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+ cutoff = params["pvalCutoff"], |
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+ colours = annot2col(params), path = "qualVarAnalysis/", |
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+ filename = "qualVar", typeImage = "png") |
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+} |
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+\arguments{
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+ \item{params}{An object of class
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+ \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
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+ providing the parameters of the analysis.} |
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+ |
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+ \item{icaSet}{An object of class
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+ \code{\link[MineICA:IcaSet-class]{IcaSet}}.}
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+ |
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+ \item{keepVar}{The variable labels to be considered, must
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+ be a subset of \code{varLabels(icaSet)}.}
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+ |
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+ \item{keepComp}{A subset of components, must be included
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+ in \code{indComp(icaSet)}. By default, all components are
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+ used.} |
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+ |
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+ \item{keepSamples}{A subset of samples, must be included
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+ in \code{sampleNames(icaSet)}. By default, all samples
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+ are used.} |
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+ |
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+ \item{adjustBy}{The way the p-values of the Wilcoxon and
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+ Kruskal-Wallis tests should be corrected for multiple |
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+ testing: \code{"none"} if no p-value correction has to be
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+ done, \code{"component"} if the p-values have to be
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+ corrected by component, \code{"variable"} if the p-values
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+ have to be corrected by variable} |
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+ |
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+ \item{method}{The correction method, see
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+ \code{\link{p.adjust}} for details, default is
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+ \code{"BH"} for Benjamini & Hochberg.}
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+ |
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+ \item{doPlot}{If TRUE (default), the plots are done, else
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+ only tests are performed.} |
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+ |
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+ \item{addPoints}{If TRUE, points are superimposed on the
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+ boxplot.} |
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+ |
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+ \item{typePlot}{The type of plot, either \code{"density"}
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+ or \code{"boxplot"}.}
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+ |
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+ \item{onlySign}{If TRUE (default), only the significant
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+ results are plotted.} |
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+ |
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+ \item{cutoff}{A threshold p-value for statistical
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+ significance.} |
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+ |
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+ \item{colours}{A vector of colours indexed by the
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+ variable levels, if missing the colours are automatically |
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+ generated using \code{\link{annot2Color}}.}
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+ |
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+ \item{path}{A directory _within resPath(params)_ where
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+ the files containing the plots and the p-value results |
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+ will be located. Default is \code{"qualVarAnalysis/"}.}
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+ |
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+ \item{typeImage}{The type of image file to be used.}
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+ |
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+ \item{filename}{The name of the HTML file containing the
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+ p-values of the tests, if NULL no file is created.} |
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+} |
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+\value{
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+ Returns A data.frame of dimensions 'components x |
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+ variables' containing the p-values of the non-parametric |
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+ tests (Wilcoxon or Kruskal-Wallis tests) wich test if the |
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+ samples groups defined by each variable are differently |
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+ distributed on the components. |
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+} |
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+\description{
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+ This function tests if the groups of samples formed by |
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+ the variables are differently distributed on the |
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+ components, in terms of contribution value (i.e of values |
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+ in matrix \code{A(icaSet)}). The distribution of the
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+ samples on the components are represented using either |
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+ density plots of boxplots. It is possible to restrict the |
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+ tests and the plots to a subset of samples and/or |
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+ components. |
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+} |
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+\details{
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+ This function writes an HTML file containing the results |
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+ of the tests as a an array of dimensions 'variables * |
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+ components' containing the p-values of the tests. When a |
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+ p-value is considered as significant according to the |
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+ threshold \code{cutoff}, it is written in bold and filled
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+ with a link pointing to the corresponding plot. One image |
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+ is created by plot and located into the sub-directory |
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+ "plots/" of \code{path}. Each image is named by
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+ index-of-component_var.png. Wilcoxon or Kruskal-Wallis |
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+ tests are performed depending on the number of groups of |
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+ interest in the considered variable (argument |
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+ \code{keepLev}).
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+} |
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+\examples{
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+## load an example of IcaSet |
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+data(icaSetCarbayo) |
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+ |
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+## build MineICAParams object |
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+params <- buildMineICAParams(resPath="carbayo/") |
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+ |
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+## Define the directory containing the results |
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+dir <- paste(resPath(params), "comp2annot/", sep="") |
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+ |
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+## Run tests, make no adjustment of the p-values, |
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+# for variable grade and components 1 and 2, |
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+# and plot boxplots when 'doPlot=TRUE'. |
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+qualVarAnalysis(params=params, icaSet=icaSetCarbayo, adjustBy="none", typePlot="boxplot", |
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+ keepVar="GRADE", keepComp=1:2, path=dir, doPlot=FALSE) |
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+} |
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+\author{
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+ Anne Biton |
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+} |
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+\seealso{
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+ , \code{\link{qualVarAnalysis}}, \code{\link{p.adjust}},
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+ \code{link{writeHtmlResTestsByAnnot}},
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+ \code{wilcox.test}, \code{kruskal.test}
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+} |
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+ |