eg2sym: Conversion between Entrez Gene IDs and official gene symbols...
In gage: Generally Applicable Gene-set Enrichment for Pathway Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2	eg2sym(eg) sym2eg(sym)

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

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.

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

Weijun Luo <luo_weijun@yahoo.com>

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

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

#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)

[1] "10000"     "10001"     "10002"     "10003"     "100048912" "10004"    
[1] "AKT3"     "MED6"     "NR2E3"    "NAALAD2"  "CDKN2BAS" "NAALADL1"
$`hsa00010 Glycolysis / Gluconeogenesis`
[1] "AKR1A1" "ADH1A"  "ADH1B"  "ADH1C"  "ADH4"   "ADH5"  

$`hsa00020 Citrate cycle (TCA cycle)`
[1] "CS"   "DLAT" "DLD"  "DLST" "FH"   "IDH1"

$`hsa00030 Pentose phosphate pathway`
[1] "FBP1"    "PRPS1L1" "ALDOA"   "ALDOB"   "RPIA"    "ALDOC"