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Question: Retrieving all entrez identifiers that are annotated in KEGG pathways
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gravatar for James W. MacDonald
5.7 years ago by
United States
James W. MacDonald48k wrote:
Hi Anirban, > library(hgu133plus2.db) > x <- select(hgu133plus2.db, Lkeys(hgu133plus2PATH), c("ENTREZID","PATH")) Warning message: In .generateExtraRows(tab, keys, jointype) : 'select' resulted in 1:many mapping between keys and return rows > head(x) PROBEID ENTREZID PATH 1 1007_s_at 780 <na> 2 1053_at 5982 03030 3 1053_at 5982 03420 > egids <- unique(x$ENTREZID[!is.na(x$PATH)]) > length(egids) [1] 5498 Best, Jim On 3/2/2013 8:20 AM, Anirban [guest] wrote: > Dear all, > > Is there any way to get all entrez identifiers that are annotated with KEGG pathways? Actually I am using GOStats package in R to perform KEGG pathway enrichment analysis.. In general, for each KEGG pathway term there is a list of annotated hgnc symbols or entrez identifiers.. For all KEGG pathway terms we must have one list of entrez identifiers. I want to have that list... > > What I am doing write now is as follows: > library(biomaRt) > library("GO.db") > library("KEGG.db") > library("GOstats") > library("hgu133plus2.db") > library("EMA") > library("fdrtool") > library("org.Hs.eg.db") > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > x<- hgu133plus2PATH > mapped_probes<- mappedkeys(x) > > b<-getBM(attributes=c("hgnc_symbol"),filters="affy_hg_u133_plus_2",v alues=mapped_probes,mart=ensembl) > > Is it the correct way to do that? > > Thanks in advance.. :) > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink modified 5.7 years ago by ANIRBAN BHAR60 • written 5.7 years ago by James W. MacDonald48k
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gravatar for ANIRBAN BHAR
5.7 years ago by
ANIRBAN BHAR60
ANIRBAN BHAR60 wrote:
Hi James, Thanks a lot.. Best regards, Anirban On Sat, Mar 2, 2013 at 7:41 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Anirban, > > > library(hgu133plus2.db) > > x <- select(hgu133plus2.db, Lkeys(hgu133plus2PATH), c("ENTREZID","PATH")) > Warning message: > In .generateExtraRows(tab, keys, jointype) : > 'select' resulted in 1:many mapping between keys and return rows > > head(x) > PROBEID ENTREZID PATH > 1 1007_s_at 780 <na> > 2 1053_at 5982 03030 > 3 1053_at 5982 03420 > > > egids <- unique(x$ENTREZID[!is.na(x$**PATH)]) > > length(egids) > [1] 5498 > > > Best, > > Jim > > > > > > On 3/2/2013 8:20 AM, Anirban [guest] wrote: > >> Dear all, >> >> Is there any way to get all entrez identifiers that are annotated with >> KEGG pathways? Actually I am using GOStats package in R to perform KEGG >> pathway enrichment analysis.. In general, for each KEGG pathway term there >> is a list of annotated hgnc symbols or entrez identifiers.. For all KEGG >> pathway terms we must have one list of entrez identifiers. I want to have >> that list... >> >> What I am doing write now is as follows: >> library(biomaRt) >> library("GO.db") >> library("KEGG.db") >> library("GOstats") >> library("hgu133plus2.db") >> library("EMA") >> library("fdrtool") >> library("org.Hs.eg.db") >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> x<- hgu133plus2PATH >> mapped_probes<- mappedkeys(x) >> >> b<-getBM(attributes=c("hgnc_**symbol"),filters="affy_hg_** >> u133_plus_2",values=mapped_**probes,mart=ensembl) >> >> Is it the correct way to do that? >> >> Thanks in advance.. :) >> >> -- output of sessionInfo(): >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- ______________________________________ Anirban Bhar Department of Bioinformatics University of Goettingen Goettingen, Germany [[alternative HTML version deleted]]
ADD COMMENTlink written 5.7 years ago by ANIRBAN BHAR60
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