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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+\name{writeProjByComp}
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+\alias{writeProjByComp}
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+\title{writeProjByComp}
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+\description{This function writes in an html file the description of the
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+ features, or genes, that contribute to each component. It also writes |
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+ an html file containing, for each feature or gene, its projection value on every component.} |
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+\usage{writeProjByComp(icaSet, params, mart = useMart(biomart = "ensembl",
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+ dataset = "hsapiens_gene_ensembl"), typeRetrieved = NULL, addNbOcc = |
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+ TRUE, selectionByComp = NULL, level = c("features", "genes"), typeId, selCutoffWrite=2.5)}
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+\arguments{
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+ \item{icaSet}{An object of class \code{\link{IcaSet}}}
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+ \item{params}{An object of class \code{\link{MineICAParams}} containing the
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+ parameters of the analysis. The files are written in the path |
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+ \code{genesPath(params)}. \code{selCutoff(params)} is used to select the features or genes
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+ by component.} |
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+ \item{mart}{An output of function \code{\link[biomaRt]{useMart}}
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+ containing the database used for annotation.} |
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+ \item{typeRetrieved}{The annotations biomaRt is queried about. They
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+ describe the feature or gene IDs of the argument \code{icaSet}, see \code{\link[biomaRt]{listFilters}}.}
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+ \item{addNbOcc}{If TRUE, the number of components the features/genes
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+ contribute to is added to the output. A gene/feature is considered |
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+ as a contributor of a component if its absolute scaled projection |
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+ value is higher than \code{selCutoff(icaSet)}.}
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+ \item{selectionByComp}{A list containing the feature/gene projections
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+ on each component, already restricted to the ones considered as contributors.} |
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+ \item{level}{The data level of \code{icaSet} that will be annotated:
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+ either the feature projections ("features"), or the gene projections ("genes").}
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+ \item{typeId}{The type of ID the features or the genes of
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+ \code{icaSet} correspond to. By default \code{typeID(icaSet)} is used. It must be provided in the biomaRt way
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+ (type \code{listFilters(mart)} to choose the appropriate value).}
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+ \item{selCutoffWrite}{The cutoff applied to the absolute projection values to select the features/genes that will be annotated using package \code{biomaRt}, default is 2.5.}
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+} |
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+\details{One file is created by component, each file is named by the
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+ index of the components (\code{indComp(icaSet)}) and located in the
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+ path \code{genePath(params)}.
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+ |
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+In case you are interested in writing the description of features and |
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+their annotations, please remember to modify code{genesPath(params)}, or
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+the previous files will be overwritten. |
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+ |
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+The genes are ranked according to their absolute projection values. |
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+ |
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+This function also writes an html file named "genes2comp" |
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+providing, for each feature or gene, the number of components it |
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+contributes to (according to the threshold \code{cutoffSel(params)}),
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+and its projection value on all the components. |
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+The projection values are scaled. |
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+ |
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+See function \code{\link{writeGenes}} for details.
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+} |
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+\value{This function returns a list of two elements:\describe{
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+ \item{listAnnotComp:}{a list with the output of
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+ \code{\link{writeGenes}} for each component}
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+ \item{nbOccInComp:}{a data.frame storing the projection
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+ values of each feature/gene (row) across all the components |
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+ (columns).}} |
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+} |
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+\examples{
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+\dontrun{
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+## load IcaSet object |
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+## We will use 'icaSetCarbayo', whose features are hgu133a probe sets |
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+## and feature annotations are Gene Symbols. |
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+data(icaSetCarbayo) |
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+ |
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+## define database to be used by biomaRt |
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+mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") |
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+ |
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+## define the parameters of the analysis |
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+params <- buildMineICAParams(resPath="~/resMineICACarbayo/", selCutoff=0) |
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+ |
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+## Make sure the elements "_biomaRt" of attribute 'typeID' are defined |
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+typeID(icaSetCarbayo) |
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+ |
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+### Query biomaRt and write gene descriptions in HTML files |
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+### The files will be located in the directory 'genesPath(params)' |
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+ |
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+## 1. Write description of genes |
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+res <- writeProjByComp(icaSet=icaSetCarbayo, params=params, mart=mart, |
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+ level="genes") #, typeId="hgnc_symbol") |
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+ |
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+## 2. Write description of features |
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+# change attribute 'genesPath' of params to preserve the gene descriptions |
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+genesPath(params) <- paste(resPath(params),"comp2features/",sep="") |
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+res <- writeProjByComp(icaSet=icaSetCarbayo, params=params, mart=mart, |
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+ level="features") #, typeId="affy_hg_u133a") |
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+ |
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+} |
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+} |
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+ |
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+\author{Anne Biton}
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+ |
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+\seealso{\code{\link{writeGenes}}, \code{getBM}, \code{listFilters}, \code{listAttributes}, \code{useMart}, \code{\link{selectContrib}}, \code{\link{nbOccInComp}}}
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+ |