egSymb {gage} | R Documentation

## Mapping between Entrez Gene IDs and official symbols

### Description

A two column matrix listing the Entrez IDs and official symbols for all currently known human genes.

### Usage

    data(egSymb)

### Format

The format is: chr [1:40784, 1:2] "1" "10" "100" "1000" ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:2] "eg" "sym"

### Details

This mapping matrix is commonly used together with functions `eg2sym` and `sym2eg`. Check the examples below.

### Source

This mapping data matrix were compiled using the gene data from NCBI Entrez Gene database.

Similar information can also be derived from Bioconductor package org.Hs.eg.db. Please check the package for more information.

### References

Entrez Gene <URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>

### 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 2.28.2 Index]