[BioC] Error while mapping SYMBOLS to ENTREZID
Atul Kakrana
atulkakrana at outlook.com
Fri Aug 15 04:58:16 CEST 2014
Hi All,
I am getting a strange error converting Gene Symbols to Entrez ID. Here
is my code:
>testData = read.delim("IL_CellVar.txt",head=T,row.names = 2)
> testData[1:5,1:3]
ClustID Genes.Symbol ChrLoc
NM_001034168.1 4 Ank2 chrNA:-1--1
NM_013795.4 4 Atp5l chrNA:-1--1
NM_018770 4 Igsf4a chrNA:-1--1
NM_146150.2 4 Nrd1 chrNA:-1--1
NM_134065.3 4 Epdr1 chrNA:-1--1
> clustNum = 5
> filteredClust = testData[testData$ClustID == clustNum,]
> any(is.na(filteredClust$Genes.Symbol))
[1] FALSE
> selectedEntrezIds <-
unlist(mget(filteredClust$Genes.Symbol,org.Mm.egSYMBOL2EG))
Error in unlist(mget(filteredClust$Genes.Symbol, org.Mm.egSYMBOL2EG)) :
error in evaluating the argument 'x' in selecting a method for
function 'unlist': Error in .checkKeysAreWellFormed(keys) :
keys must be supplied in a character vector with no NAs
Another approach fails too:
> selectedEntrezIds = select(org.Mm.eg.db,filteredClust$Genes.Symbol,
"ENTREZID")
Error in .select(x, keys, columns, keytype = extraArgs[["kt"]], jointype
= jointype) :
'keys' must be a character vector
I am not sure why I am getting this error as the master file from which
gene symbols were extracted for testData gives no problem while
converting to EntrezID. Would apprecite help on this.
Thanks
AK
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