buildIcaSet {MineICA} | R Documentation

## This function builds an object of class `IcaSet`.

### Description

This function builds an object of class `IcaSet`.

### Usage

      buildIcaSet(params, A, S, dat, pData = new("data.frame"),
        fData = new("data.frame"), witGenes = new("character"),
        compNames = new("character"),
        refSamples = new("character"),
        annotation = new("character"),
        chipManu = new("character"),
        chipVersion = new("character"), alreadyAnnot = FALSE,
        typeID = c(geneID_annotation = "SYMBOL", geneID_biomart = "hgnc_symbol", featureID_biomart = ""),
        runAnnot = TRUE, organism = "Human",
        mart = new("Mart"))

### Arguments

`params` | An object of class `MineICAParams` containing the parameters of the analysis
`A` | The mixing matrix of the ICA decomposition (of dimension samples x components).
`S` | The source matrix of the ICA decomposition (of dimension features x components).
`dat` | The data matrix the ICA was applied to (of dimension features x samples).
`pData` | Phenotype data, a data.frame which contains the sample informations of dimension samples x annotations.
`fData` | Feature data, a data.frame which contrains the feature descriptions of dimensions features x annotations.
`witGenes` | A vector of witness genes. They are representative of the expression behavior of the contributing genes of each component. If missing or NULL, they will be automatically attributed using function `selectWitnessGenes`.
`compNames` | A vector of component labels.
`refSamples` | A vector of reference sample IDs (e.g the "normal" samples).
`annotation` | An annotation package (e.g a ".db" package specific to the microarray used to generate `dat`)
`chipManu` | If microarray data, the manufacturer: either 'affymetrix' or 'illumina'.
`chipVersion` | For illumina microarrays: the version of the microarray.
`alreadyAnnot` | TRUE if the feature IDs contained in the row names of `dat` and `S` already correspond to the final level of annotation (e.g if they are already gene IDs). In that case, no annotation is performed.
`typeID` | A character vector specifying the annotation IDs, it includes three elements : geneID_annotation the IDs from the package to be used to annotate the features into genes. It will be used to fill the attributes `datByGene` and `SByGene` of the `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. geneID_biomart the type of gene IDs, as available in `listFilters(mart)`; where mart is specified as described in `useMart`. If you have directly built the IcaSet at the gene level (i.e if no annotation package is used), `featureID_biomart` and `geneID_biomart` will be identical. featureID_biomart the type of feature IDs, as available in `listFilters(mart)`; where `mart` is specified as described in function `useMart`. Not useful if you work at the gene level.
`runAnnot` | If TRUE, `icaSet` is annotated with function `annotInGene`.
`organism` | The organism the data correspond to.
`mart` | The mart object (database and dataset) used for annotation, see function `useMart` of package `biomaRt`

### Value

An object of class IcaSet

### Author(s)

Anne Biton

### See Also

`selectWitnessGenes`, `annotInGene`

### Examples

    dat <- data.frame(matrix(rnorm(10000),ncol=10,nrow=1000))
    rownames(dat) <- paste("g", 1:1000, sep="")
    colnames(dat) <- paste("s", 1:10, sep="")

    ## build a data.frame containing sample annotations
    annot <- data.frame(type=c(rep("a",5),rep("b",5)))
    rownames(annot) <- colnames(dat)

    ## run ICA
    resJade <- runICA(X=dat, nbComp=3, method = "JADE")

    ## build params
    params <- buildMineICAParams(resPath="toy/")

    ## build IcaSet object
    icaSettoy <- buildIcaSet(params=params, A=data.frame(resJade$A), S=data.frame(resJade$S),
                             dat=dat, pData=annot, alreadyAnnot=TRUE)
    params <- icaSettoy$params
    icaSettoy <- icaSettoy$icaSet

    ## Not run:
    ## load data
    library(breastCancerMAINZ)
    data(mainz)

    ## run ICA
    resJade <- runICA(X=dataMainz, nbComp=10, method = "JADE", maxit=10000)

    ## build params
    params <- buildMineICAParams(resPath="mainz/")

    ## build IcaSet object

    # fill typeID, Mainz data originate from affymetrix HG-U133a  microarray and are indexed by probe sets
    # we want to annotate the probe sets into Gene Symbols
    typeIDmainz <-  c(geneID_annotation="SYMBOL", geneID_biomart="hgnc_symbol", featureID_biomart="affy_hg_u133a")

    icaSetMainz <- buildIcaSet(params=params, A=data.frame(resJade$A), S=data.frame(resJade$S),
                                 dat=exprs(mainz), pData=pData(mainz),
                                 annotation="hgu133a.db", typeID= c(geneID_annotation = "SYMBOL",
                                 geneID_biomart = "hgnc_symbol", featureID_biomart = "affy_hg_u133a"),
                                 chipManu = "affymetrix", runAnnot=TRUE,
                                 mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl"))

    ## End(Not run)

[Package MineICA version 1.34.0 Index]