annotate {mAPKL} | R Documentation

## Genome annotation of the "exemplars".

### Description

The user may extract several genome specific information for the "exemplars" as described in the microarray annotation file.

### Usage

        annotate(exemplars,chip)

### Arguments

`exemplars` | The "exemplars" of the mAPKL class.
`chip` | The platforms's name of the microarray chip used (e.g. "hgu133plus2.db")

### Details

This function uses as key the probe id and returns the mathing information as described in the gene chip annotation file. The returned information are ussually multiple to the number of probe ids (one to many relationship) and are stored in the results. In the rest items only the first of the returned values are stored.

### Value

`results` | The accumulated annotation results.
`probe` | The probe id.
`symbol` | The official gene symbol.
`entrezId` | The Entrez gene Identifier.
`ensemblId` | The ensembl ID as indicated by ensembl.
`map` | The cytoband locations of the gene.

### Author(s)

Argiris Sakellariou

### Examples

    ## We use the "exemplars" from the mAPKL.Rd example

    exemplrs <- c(24, 26, 42, 45, 63, 81, 95, 99, 102, 113, 134, 135, 145, 152, 168)
    names(exemplrs)<- c("215717_s_at", "1561358_at", "222752_s_at", "233922_at",
    "218871_x_at", "33323_r_at", "244311_at", "220932_at", "205508_at", "209596_at",
    "215180_at", "1560638_a_at", "201852_x_at", "229947_at", "221731_x_at")

    gene.info <- annotate(exemplrs,"hgu133plus2.db")

[Package mAPKL version 1.20.0 Index]