Hi,
I have a simple problem that's driving me nuts... Any hints are appreciated!

I am retrieving the human homologues of rat genes. I use the functions 'getHOMOLOG' and 'listToCharacterVector' from the library annotationTools. Everything is going fine, except for one thing:
Some rows (genes) contain multiple entries (homologues); for such row I would like to get rid of all entries except the first one.
Example: for row 18634 I currently have:
[18634] "6173 /// 100529097"

I would like to get rid of everything except the first entry, so to get this:
[18634] "6173"

How to do this for all relevant rows? Basically, I thus would like to remove everything positioned after the first number, starting with space-3xforwardslash-etc.
Thanks,
Guido


library(annotationTools)
library(hugene11stv1hsentrezg.db)
library(ragene11stv1rnentrezg.db)

#Download HomoloGene data from:
#ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/
homologene<-read.delim("homologene.data.121212.data",header=FALSE)  # (date of file manually added to name when saving download)
colnames (homologene) <- c ("HomologyGroupID", "TaxonID", "EgID", "Symbol", "ProteinGI", "ProteinAcc")

# Read rat probesets that are on the array as Entrez IDs; this returns a list which is converted to a character vector
# Next the probesets that don't have an EntrezID are removed
rat.eg.array <- mget(ls(ragene11stv1rnentrezgENTREZID), ragene11stv1rnentrezgENTREZID)
rat.eg.array <- listToCharacterVector(rat.eg.array)
rat.eg.array <- rat.eg.array[!is.na(rat.eg.array)]

# Convert rat EG IDs into human (9606) homologs; this returns a list which is converted to a character vector
> rat2human <- getHOMOLOG(rat.eg.array,9606,homologene) #this takes some time
Warning messages:
1: In getHOMOLOG(rat.eg.array, 9606, homologene) :
  One or more gene input gene ID/cluster not found in homologue table
2: In getHOMOLOG(rat.eg.array, 9606, homologene) :
  One or more gene ID/cluster with no target provided in homologue table
> rat2human <- listToCharacterVector(rat2human)
> class(rat2human)
[1] "character"
>
> head(rat2human)
[1] "54552"  "80212"  "11277"  "10663"  "199692" "399947"
>
> #example of multiple entries
> rat2human[18634]
[1] "6173 /// 100529097"
>



---------------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
email:      guido.hooiveld@wur.nl
internet:   http://nutrigene.4t.com
http://scholar.google.com/citations?user=qFHaMnoAAAAJ
http://www.researcherid.com/rid/F-4912-2010


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