@@ -318,7 +318,7 @@

 \seealso{

   \code{\link{eSet-class}}, \code{\link{buildIcaSet}},

-  \code{\link{IcaSet-class}}, \code{\link{MineICAParams-class}}.

+  \code{\link{class-IcaSet}}, \code{\link{class-MineICAParams}}.

 }

 \examples{

@@ -23,10 +23,6 @@

 \alias{organism<-}

 \alias{organism,IcaSet-method}

 \alias{organism<-,IcaSet-method}

-\alias{organism<-,IcaSet,character-method}

-\alias{setOrganism,IcaSet-method}

-\alias{getOrganism,IcaSet-method}

-

 \alias{mart}

 \alias{mart<-}

new file mode 100644

@@ -0,0 +1,341 @@

+\name{IcaSet}

+\docType{class}

+\alias{class:IcaSet}

+\alias{IcaSet}

+\alias{IcaSet-class}

+

+%\alias{dat}  % pour la generique

+%\alias{dat,IcaSet-method}% # avec la signature de ma classe

+%\alias{dat<-} %# la generique de remplacement

+%\alias{dat<-,IcaSet,matrix-method} %# avec la signature de la classe 

+

+\alias{[}

+\alias{[,ANY,ANY,IcaSet-method}

+\alias{[,IcaSet,ANY-method} 

+\alias{[,IcaSet,ANY,ANY-method} 

+\alias{[,IcaSet,ANY,ANY,ANY-method} 

+\alias{[<-}

+\alias{[<-,IcaSet,ANY,ANY,ANY,ANY-method} 

+\alias{[<-,IcaSet,ANY,ANY,ANY-method} 

+\alias{[<-,IcaSet,ANY,ANY-method} 

+

+\alias{organism}

+\alias{organism<-}

+\alias{organism,IcaSet-method}

+\alias{organism<-,IcaSet-method}

+\alias{organism<-,IcaSet,character-method}

+\alias{setOrganism,IcaSet-method}

+\alias{getOrganism,IcaSet-method}

+

+

+\alias{mart}

+\alias{mart<-}

+\alias{mart,IcaSet-method}

+\alias{mart<-,IcaSet-method}

+\alias{mart<-,IcaSet,character-method}

+\alias{setMart,IcaSet-method}

+\alias{getMart,IcaSet-method}

+

+\alias{chipVersion}

+\alias{chipVersion,IcaSet-method}

+\alias{chipVersion<-}

+\alias{chipVersion<-,IcaSet-method}

+\alias{chipVersion<-,IcaSet,character-method}

+

+%\alias{indComp}

+%\alias{indComp<-}

+\alias{indComp,IcaSet-method}

+\alias{setIndComp,IcaSet-method}

+\alias{getIndComp,IcaSet-method}

+\alias{indComp<-,IcaSet,character-method}

+%\alias{compNames}

+%\alias{compNames<-}

+\alias{compNames,IcaSet-method}

+\alias{setLabelsComp,IcaSet-method}

+\alias{getLabelsComp,IcaSet-method}

+\alias{compNames<-,IcaSet,character-method}

+%\alias{witGenes}

+%\alias{witGenes<-}

+\alias{witGenes,IcaSet-method}

+%\alias{setWitGenes,IcaSet-method}

+%\alias{getWitGenes,IcaSet-method}

+\alias{witGenes<-,IcaSet,character-method}

+\alias{refSamples}

+\alias{refSamples<-}

+\alias{refSamples,IcaSet-method}

+\alias{setRefSamples,IcaSet-method}

+\alias{getRefSamples,IcaSet-method}

+\alias{refSamples<-,IcaSet-method}

+\alias{refSamples<-,IcaSet,character-method}

+\alias{typeID}

+\alias{typeID<-}

+\alias{typeID,IcaSet-method}

+\alias{typeID<-,IcaSet-method}

+\alias{setTypeID,IcaSet-method}

+\alias{getTypeID,IcaSet-method}

+\alias{typeID<-,IcaSet,list-method}

+\alias{chipManu}

+\alias{chipManu<-}

+\alias{chipManu<-,IcaSet-method}

+\alias{chipManu<-,IcaSet,character-method}

+\alias{chipManu,IcaSet-method}

+\alias{setChipManu,IcaSet-method}

+\alias{getChipManu,IcaSet-method}

+

+

+\alias{Slist,IcaSet-method}

+\alias{SlistByGene,IcaSet-method}

+\alias{Alist,IcaSet-method}

+

+

+

+\title{

+  Class to Contain and Describe an ICA decomposition of High-Throughput Data.

+}

+

+\description{

+  Container for high-throughput data and results of ICA decomposition

+  obtained on these data. \code{IcaSet} class is derived from

+  \code{\link{eSet}}, and requires a matrix named \code{dat} as

+  \code{assayData} member.

+}

+\section{Extends}{

+   Directly extends class \code{\link{eSet}}.

+}

+\section{Creating Objects}{

+

+  \code{new("IcaSet")}

+

+  \code{new("IcaSet",

+    annotation = character(0),

+    experimentData = new("MIAME"),

+    featureData = new("AnnotatedDataFrame"),

+    phenoData = new("AnnotatedDataFrame"),

+    protocolData = phenoData[,integer(0)],

+    dat = new("matrix"),

+    A=new("data.frame"),

+    S=new("data.frame"), ...)

+    }

+

+  This creates an \code{IcaSet} with \code{assayData} implicitly

+  created to contain \code{dat}. %Additional named matrix arguments

+  %with the same dimensions as \code{dat} are added to

+  %\code{assayData}; the row and column names of these additional

+  %matrices should match those of \code{dat}. 

+

+  \code{new("IcaSet",

+    annotation = character(0),

+    assayData = assayDataNew(dat=new("matrix")),

+    experimentData = new("MIAME"),

+    featureData = new("AnnotatedDataFrame"),

+    phenoData = new("AnnotatedDataFrame"),

+    protocolData = phenoData[,integer(0)],

+    A=new("data.frame"),

+    S=new("data.frame"), ...)

+  }

+

+  This creates an \code{IcaSet} with \code{assayData} provided

+  explicitly. %In this form, the only required named arguments are \code{assayData}.

+

+

+  \code{IcaSet} instances are usually created through

+  \code{new("IcaSet", ...)}. Usually the arguments to \code{new}

+  include \code{dat} ('features x samples', e.g a matrix of expression

+  data), \code{phenoData} ('samples x annotations', a

+  matrix of sample annotations), \code{S} the Source

+  matrix of the ICA decomposition ('features x comp'), \code{A} the Mixing matrix of the ICA

+  decomposition ('samples x comp'), \code{annotation} the annotation

+  package, \code{typeID} the description of the feature and gene IDs.  

+

+  The other attributes can be missing, in which case

+  they are assigned default values.

+

+  The function \code{\link{buildIcaSet}} is a more convenient way to

+  create \code{IcaSet} instances, and allows to automatically annotate

+  the features.

+}

+\section{Slots}{

+  Inherited from \code{eSet}:

+  \describe{

+    \item{\code{annotation}:}{See \code{\link{eSet}}}

+    \item{\code{assayData}:}{Contains matrices with equal

+      dimensions, and with column number equal to

+      \code{nrow(phenoData)}. \code{assayData} must contain a matrix

+      \code{dat} with rows representing features (e.g., reporters)

+      and columns representing samples. Class:\code{\link{AssayData-class}}}

+    \item{\code{experimentData}:}{See \code{\link{eSet}}}

+    \item{\code{featureData}:}{See \code{\link{eSet}}}

+    \item{\code{phenoData}:}{See \code{\link{eSet}}}

+    \item{\code{protocolData}:}{See \code{\link{eSet}}}

+  

+  Specific slot:

+

+    \item{\code{organism}:}{Contains the name of the species. Currently

+  only Human ("Human" or "Homo sapiens") and Mouse ("Mouse" or "Mus

+  musculus") are supported. Only used when \code{chipManu}="illumina"

+  }

+    \item{\code{mart}:}{An output of \code{\link[biomaRt]{useMart}} of package \code{biomaRt}. Only useful if no annotation package is available for argument \code{icaSet}.

+  }

+  

+  \item{\code{datByGene}:}{Data.frame containing the data \code{dat} where

+  features have been replaced by their annotations (e.g, gene IDs). Rows 

+  represent annotations of the features (e.g., gene IDs) and

+  columns represent samples.}

+  \item{\code{A}:}{The mixing matrix of the ICA decomposition, contained

+  in a data.frame whose

+  column number equals the number of components and row number equals

+  \code{nrow(phenoData)} (dimension: 'samples x comp').}

+  \item{\code{S}:}{The source matrix of the ICA decomposition, contained

+  in a data.frame whose

+  column number equals the number of components and row number equals

+  \code{nrow(assayData)} (dimension: 'features x comp').}

+  \item{\code{SByGene}:}{The matrix Source of the ICA decomposition, contained

+  in a data.frame whose

+  column number equals the number of components and row number equals

+  \code{nrow(datByGene)} (dimension: 'annotatedFeatures x comp').}

+  \item{\code{compNames}:}{A vector of component labels with length

+  equal to the number of component.}

+  \item{\code{indComp}:}{A vector of component indices with length

+  equal to the number of component.}

+  \item{\code{witGenes}:}{A vector of gene IDs with length

+  equal to the number of component.}

+  \item{\code{chipManu}:}{The manufacturer of the technology the

+  data originates from. Useful for the annotation of the features when

+  data originates from an _illumina_ microarray.}

+  \item{\code{chipVersion}:}{The version of the chip, only useful for

+  when \code{chipManu}="illumina"}

+   \item{\code{refSamples}:}{A vector of sample IDs including the reference samples, e.g the "normal" samples.

+  Must be included in \code{sampleNames(object)}, i.e in \code{colnames(dat)}.}

+   \item{\code{typeID}:}{A vector of characters providing the annotation IDs. It includes

+     three elements:

+ \describe{ 

+ \item{geneID_annotation}{the IDs from the

+ package to be used to annotate the features into genes. It will be used to

+ fill the attributes \code{datByGene} and \code{SByGene} of the \code{icaSet}.

+ It must match one of the objects the corresponding package supports

+ (you can access the list of objects by typing ls("package:packagename")). If

+ no annotation package is provided, this element is not useful.}

+ \item{geneID_biomart}{the type of gene IDs, as available in

+ \code{listFilters(mart)}; where mart is specified as described in \code{\link[biomaRt]{useMart}}.

+ If you have directly built the IcaSet at the

+ gene level (i.e if no annotation package is used), \code{featureID_biomart} and

+ \code{geneID_biomart} will be identical.} 

+ \item{featureID_biomart}{the

+ type of feature IDs, as available in \code{listFilters(mart)}; where

+ \code{mart} is specified as described in function \code{\link[biomaRt]{useMart}}.

+ Not useful if you work at the gene level.} }}

+

+}

+}

+\section{Methods}{

+  

+  Class-specific methods.

+  \describe{

+   

+      \item{\code{getComp(IcaSet, ind,

+      level=c("features","genes"))}}{Given a component index, extract

+      the corresponding sample contribution values from A, and the

+      feature (\code{level}="features") or gene (\code{level}="genes")

+      projections from S. Returns a list with two elements:

+      \code{contrib} the sample contributions and \code{proj} the

+      feature or gene projections.}

+     

+     Access and set any slot specific to IcaSet:

+     \item{\code{slotName(IcaSet)}, and

+       \code{slotName(IcaSet)<-}:}{Accessing and setting any slot

+       of name \code{slotName} contained in an IcaSet object.}

+     

+    \item{\code{IcaSet["slotName"]}, and

+       \code{IcaSet["slotName"]<-}:}{Accessing and setting any slot

+       of name \code{slotName} contained in an IcaSet object.}

+     

+     Most used accessors and settors:

+     \item{\code{A(IcaSet)}, and

+       \code{A(IcaSet)<-}:}{Accessing and setting Mixing matrix \code{A}.}

+     \item{\code{S(IcaSet)}, and

+       \code{S(IcaSet)<-}:}{Accessing and setting

+       the data.frame Source \code{S}.}

+     \item{\code{Slist(IcaSet)}:}{Accessing

+       the data.frame Source as a list where names are preserved.}

+     \item{\code{SByGene(IcaSet)}, and

+       \code{SByGene(IcaSet)<-}:}{Accessing

+       and setting the _annotated_ data.frame Source \code{SByGene}.}

+     \item{\code{SlistByGene(IcaSet)}:}{Accessing

+       the _annotated_ Source matrix as a list where names are preserved.}

+      \item{\code{organism(IcaSet)}, \code{organism(IcaSet,characte)<-}}{Access and

+	set value in the \code{organism} slot.}

+     \item{\code{dat(IcaSet)}, \code{dat(IcaSet,matrix)<-}}{Access and

+       set elements named \code{dat} in the \code{AssayData-class}

+       slot.}

+

+    }

+

+   Derived from \code{\link{eSet}}:

+   \describe{

+     \item{\code{pData(IcaSet)}, \code{pData(IcaSet,value)<-}:}{See \code{\link{eSet}}}

+     \item{\code{assayData(IcaSet)}:}{See \code{\link{eSet}}}

+     \item{\code{sampleNames(IcaSet)} and \code{sampleNames(IcaSet)<-}:}{See \code{\link{eSet}}}

+     \item{\code{featureNames(IcaSet)}, \code{featureNames(IcaSet, value)<-}:}{See \code{\link{eSet}}}

+     \item{\code{dims(IcaSet)}:}{See \code{\link{eSet}}}

+     \item{\code{phenoData(IcaSet)}, \code{phenoData(IcaSet,value)<-}:}{See \code{\link{eSet}}}

+     \item{\code{varLabels(IcaSet)}, \code{varLabels(IcaSet, value)<-}:}{See \code{\link{eSet}}}

+     \item{\code{varMetadata(IcaSet)}, \code{varMetadata(IcaSet,value)<-}:}{See \code{\link{eSet}}}

+     \item{\code{varMetadata(IcaSet)}, \code{varMetadata(IcaSet,value)}}{See \code{\link{eSet}}}

+     \item{\code{experimentData(IcaSet)},\code{experimentData(IcaSet,value)<-}:}{See \code{\link{eSet}}}

+     \item{\code{pubMedIds(IcaSet)}, \code{pubMedIds(IcaSet,value)}}{See \code{\link{eSet}}}

+     \item{\code{abstract(IcaSet)}:}{See \code{\link{eSet}}}

+     \item{\code{annotation(IcaSet)}, \code{annotation(IcaSet,value)<-}}{See \code{\link{eSet}}}

+     \item{\code{protocolData(IcaSet)}, \code{protocolData(IcaSet,value)<-}}{See \code{\link{eSet}}}

+     \item{\code{combine(IcaSet,IcaSet)}:}{See \code{\link{eSet}}}

+     \item{\code{storageMode(IcaSet)}, \code{storageMode(IcaSet,character)<-}:}{See \code{\link{eSet}}}

+   }

+  

+  Standard generic methods:

+  \describe{

+    \item{\code{initialize(IcaSet)}:}{Object instantiation, used

+      by \code{new}; not to be called directly by the user.}

+    

+    \item{\code{validObject(IcaSet)}:}{Validity-checking method, ensuring

+      that \code{dat} is a member of

+      \code{assayData}, and that the number of features, genes, samples,

+      and components are consistent across all the attributes of the

+      IcaSet object. \code{checkValidity(IcaSet)} imposes this

+      validity check, and the validity checks of \code{eSet}.}

+    \item{\code{IcaSet[slotName]}, \code{IcaSet[slotName]<-}:}{Accessing

+      and setting any slot of name \code{slotName} contained in an

+      IcaSet object.}

+    \item{\code{IcaSet[i, j, k]}:}{Extract object of class "IcaSet"

+          for features or genes with names i, samples with names or

+      indices j, and components with names or indices k.}

+       \item{\code{makeDataPackage(object, author, email, packageName, packageVersion, license, biocViews, filePath, description=paste(abstract(object), collapse="\n\n"), ...)}}{

+      Create a data package based on an IcaSet object. See

+      \code{\link{makeDataPackage}}.}

+     \item{\code{show(IcaSet)}:}{See \code{\link{eSet}}}

+     \item{\code{dim(IcaSet)}, \code{ncol}:}{See \code{\link{eSet}}}

+     \item{\code{IcaSet[(index)]}:}{See \code{\link{eSet}}}

+     \item{\code{IcaSet$}, \code{IcaSet$<-}:}{See \code{\link{eSet}}}

+     \item{\code{IcaSet[[i]]}, \code{IcaSet[[i]]<-}:}{See \code{\link{eSet}}}

+  }

+}

+

+\author{Anne Biton}

+

+\seealso{

+  \code{\link{eSet-class}}, \code{\link{buildIcaSet}},

+  \code{\link{IcaSet-class}}, \code{\link{MineICAParams-class}}.

+}

+

+\examples{

+# create an instance of IcaSet

+new("IcaSet")

+dat <- matrix(runif(100000), nrow=1000, ncol=100)

+rownames(dat) <- 1:nrow(dat)

+new("IcaSet",

+    dat=dat, 

+    A=as.data.frame(matrix(runif(1000), nrow=100, ncol=10)),

+    S=as.data.frame(matrix(runif(10000), nrow=1000, ncol=10), row.names = 1:nrow(dat)))

+

+

+}

+

+\keyword{classes}