buildIcaSet {MineICA} | R Documentation |
IcaSet
.This function builds an object of class
IcaSet
.
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"))
params |
An object of class
|
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
|
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
|
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 |
typeID |
A character vector specifying the annotation IDs, it includes three elements :
|
runAnnot |
If TRUE, |
organism |
The organism the data correspond to. |
mart |
The mart object (database and dataset) used
for annotation, see function |
An object of class IcaSet
Anne Biton
selectWitnessGenes
,
annotInGene
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)