Question: Retrieving all entrez identifiers that are annotated in KEGG pathways
6.2 years ago by
Guest User • 12k
Guest User • 12k 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",val ues=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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
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