Annotate: Gene annotation
In metaOmics/preproc: Preprocessing of Normalized Gene Expression Data

Description Usage Arguments Details Value Author(s) Examples

Annotation for the gene expression data set.

1 2	Annotate(dataset, id.type = ID.TYPE.geneSymbol, platform = "", species = "", annotation.file = NA)

`dataset`	A numeric matrix of gene expressions or a Study object. For matrix, Each row is for one gene and each column is for one sample. The rownames should be gene IDs, which could be probe IDs, refseq IDs, entrez IDs, or gene symbols. For Study object, the same rule for matrix apply to each matrix in the Study@datasets list.
`id.type`	a character string to specify the type of gene ID. It should be `"ProbeID"`, `"GeneSymbol"`, `"RefSeqID"`, or `"EntrezID"`.
`platform`	a character string to specify the platform of the gene expression data set. See details.
`species`	a character string to specify the species of the gene expression data set. The accepted `species` include `"human"`, `"mouse"`, and `"rat"`.
`annotation.file`	a character string of a txt file name to upload user-specific annotation file. The default is `NA`. See details.

Annotate will transform the row names of the dataset to gene symbol. The original row names could be either gene symbol (in the case it is already gene symbol, no tranformation take place), reference sequence, or entrez id.

For human, the accepted platforms include "chip hgu95a", "chip hgu95av2", "chip hgu95b", "chip hgu95c", "chip hgu95d", "chip hgu95e", "chip hgu133a", "chip hgu133b", "hgu133plus2", "Illumina HumanHT-12 V3 Bead Array", "Illumina HumanHT-12 V4 Bead Array", "Illumina HumanWG-6 V1 Bead Array", "Illumina HumanWG-6 V2 Bead Array", "Illumina HumanWG V2 Bead Array", "chip hgug4100a", "chip hgug4101a", "chip hgug4110b", "chip hgug4111a", and "chip hgug4112a".

For mouse, the accepted platforms include "chip mgu74a", "chip mgu74av2", "chip mgu74b", "chip mgu74bv2", "chip mgu74c", "chip mgu74cv2", "chip moe430a", "chip moe430b", "Affymetrix GeneChip Mouse Genome 430 2.0", "Illumina MouseWG-6 v1.0 Bead Array", "Illumina MouseWG-6 v2.0 Bead Array", "chip mgug4104a", "chip mgug4120a", "chip mgug4121a", and "chip mgug4122a".

For rat, the accepted platforms include "chip rat2302", "chip rgu34a", "chip rgu34b", "chip rgu34c", "Illumina Rat v1.0 Bead Array", "chip rgug4105a", "chip rgug4130a", and "chip rgug4131a".

For other platforms, an annotation file is needed to be uploaded by annotation.file. The annotation file to be read should be prepared strictly according following format. The first column should be probe ID, and the second column should be gene symbol. The first row should be the column headers.

If dataset is matrix, it returns A numeric matrix of gene expressions. with row names being genesymbol. If dataset is Study object, a Study object is returned with Study@datasets annotates.

Lin Wang, Schwannden Kuo

data(datasets.eg)
data(preproc.option)
# Annotate Expression Matrix
res <- Annotate(dataset=datasets.eg[[1]], id.type=ID.TYPE.probeID, 
                platform=PLATFORM.hgu133plus2)
# Annotate Study
study <- new("Study", name="test", dtype=DTYPE.microarray, datasets=datasets.eg[1])
res <- Annotate(study, id.type=ID.TYPE.probeID, platform=PLATFORM.hgu133plus2)