Oh, and x = rat2human, of course. On Thu 28 Feb 2013 02:23:31 PM PST, Ryan C. Thompson wrote: > You can try this: > > library(stringr) > x <- str_replace(string=x, pattern=" /// .*$", replacement="") > stopifnot(!any(str_detect(x, "///")) > > You might want to adjust the pattern to allow arbitrary spacing rather > than just single spaces. > > On Thu 28 Feb 2013 02:11:21 PM PST, Hooiveld, Guido wrote: >> 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 at wur.nl >> internet: http://nutrigene.4t.com >> http://scholar.google.com/citations?user=qFHaMnoAAAAJ >> http://www.researcherid.com/rid/F-4912-2010 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor