eg2sym {gage} | R Documentation

## Conversion between Entrez Gene IDs and official gene symbols for human genes.

### Description

These functions convert Entrez Gene IDs to official gene symbols for human genes, or vise versa.

### Usage

    eg2sym(eg)
    sym2eg(sym)

### Arguments

`eg` | character vector for Entrez Gene IDs (human genes only).
`sym` | character vector for official gene symbols (human genes only).

### Details

Currently, only conversion for human genes are supported. Notice that some gene symbols are not official, hence not recognized and NA will be returned in such cases.

### Value

A character vector giving the converted official gene symbols or Entrez IDs.

### Author(s)

Weijun Luo <luo_weijun@yahoo.com>

### References

Luo, W., Friedman, M., Shedden K., Hankenson, K. and Woolf, P GAGE: Generally Applicable Gene Set Enrichment for Pathways Analysis. BMC Bioinformatics 2009, 10:161

### See Also

`egSymb` mapping data between Entrez Gene IDs and official symbols; `readList` read in gene set list

### Examples

    #genes in gse16873 was label by Entrez IDs
    data(gse16873)
    head(rownames(gse16873))
    #may convert the gene IDs to official symbols
    gse16873.sym<-gse16873
    data(egSymb)
    rownames(gse16873.sym)<-eg2sym(rownames(gse16873.sym))
    head(rownames(gse16873.sym))

    #convert kegg.gs correspondingly
    data(kegg.gs)
    kegg.gs.sym<-lapply(kegg.gs, eg2sym)
    lapply(kegg.gs.sym[1:3],head)
    #GAGE analysis with the converted data
    cn=colnames(gse16873)
    hn=grep('HN',cn, ignore.case =TRUE)
    dcis=grep('DCIS',cn, ignore.case =TRUE)
    gse16873.kegg.p2 <- gage(gse16873.sym, gsets = kegg.gs.sym,
        ref = hn, samp = dcis)

[Package gage version 2.30.0 Index]