Looking for R script to categorize genes using GO terms
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Fangxin Hong ▴ 810
@fangxin-hong-912
Last seen 10.2 years ago
Hi Dear list, I am wondering whether someone has written some R script to categorize genes into different Go categories (e.g., replication, cell wall,...) according to gene AffyID? I am working on ATH1 array. Or any hint/ quick way to do it? Thanks in advance Fangxin -------------------- Fangxin Hong Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong at salk.edu (Phone): 858-453-4100 ext 1105
GO GO • 1.1k views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 9.6 years ago
United States
Hi, There is some documentation in the Using Data Packages, vignette, something like library(annotate) openVignette() select #5 for the pdf, the R source code is also available, through other means. Feedback etc on whether the vignette needs improvement should be sent along to the package maintainer, best wishes, Robert fhong at salk.edu wrote: > Hi Dear list, > > I am wondering whether someone has written some R script to categorize > genes into different Go categories (e.g., replication, cell wall,...) > according to gene AffyID? I am working on ATH1 array. Or any hint/ quick > way to do it? > > Thanks in advance > Fangxin > > > -------------------- > Fangxin Hong Ph.D. > Plant Biology Laboratory > The Salk Institute > 10010 N. Torrey Pines Rd. > La Jolla, CA 92037 > E-mail: fhong at salk.edu > (Phone): 858-453-4100 ext 1105 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Thanks, Robert. I made the functions myself using the handout from the short Course(this June), it turns out to be pretty simple. So I would provide the R script of doing this if somebody ask for. Good day. Fangxin > Hi, > There is some documentation in the Using Data Packages, vignette, > > something like > > library(annotate) > openVignette() > > select #5 for the pdf, the R source code is also available, through > other means. > > Feedback etc on whether the vignette needs improvement should be sent > along to the package maintainer, > > best wishes, > Robert > > > fhong at salk.edu wrote: >> Hi Dear list, >> >> I am wondering whether someone has written some R script to categorize >> genes into different Go categories (e.g., replication, cell wall,...) >> according to gene AffyID? I am working on ATH1 array. Or any hint/ quick >> way to do it? >> >> Thanks in advance >> Fangxin >> >> >> -------------------- >> Fangxin Hong Ph.D. >> Plant Biology Laboratory >> The Salk Institute >> 10010 N. Torrey Pines Rd. >> La Jolla, CA 92037 >> E-mail: fhong at salk.edu >> (Phone): 858-453-4100 ext 1105 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem at fhcrc.org > > -------------------- Fangxin Hong Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong at salk.edu (Phone): 858-453-4100 ext 1105
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@sean-davis-490
Last seen 3 months ago
United States
On 11/2/05 1:25 PM, "fhong at salk.edu" <fhong at="" salk.edu=""> wrote: > Hi Dear list, > > I am wondering whether someone has written some R script to categorize > genes into different Go categories (e.g., replication, cell wall,...) > according to gene AffyID? I am working on ATH1 array. Or any hint/ quick > way to do it? > > Thanks in advance > Fangxin Have you looked at the GOstats package and its vignettes? That is the place to start. There is metadata for ATH1 available. Sean
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Morten ▴ 300
@morten-929
Last seen 10.2 years ago
Hi... I have a script (which you can see is written by a biologist :) here :http://folk.uio.no/mortema/master.R or code (depends limma object "MA" to work) md<-get("GO:0007517", GOBPCHILDREN) myGO<-append(md,"GO:0007517") for (i in myGO){ probe<-unique(lookUp(i, "mgug4121a", "GO2ALLPROBES")) } res<-NULL for (i in probe){ res<-append(res,grep(i,MA$gene$ID)) } myM<-matrix(nrow=(length(res)),ncol=12) jens = 1 for(i in res){ myM[jens,] = MA$M[i,] jens <- jens+1 } name=NULL for (i in res){ name<-append(name,MA$gene$GeneName[i]) jens<-jens+1 } row.names(myM)<-name write.table(myM,file="muscle development.txt",sep="\t",row.names=T) #expressions values for genes involved in mucle development >Hi Dear list, > >I am wondering whether someone has written some R script to categorize >genes into different Go categories (e.g., replication, cell wall,...) >according to gene AffyID? I am working on ATH1 array. Or any hint/ quick >way to do it? > >Thanks in advance >Fangxin > > >-------------------- >Fangxin Hong Ph.D. >Plant Biology Laboratory >The Salk Institute >10010 N. Torrey Pines Rd. >La Jolla, CA 92037 >E-mail: fhong at salk.edu >(Phone): 858-453-4100 ext 1105 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >
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