eg2sym {gage} | R Documentation |
These functions convert Entrez Gene IDs to official gene symbols for human genes, or vise versa.
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)