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Question: Question about 'annFUN.db' in topGO ....
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gravatar for ALok
10.3 years ago by
ALok170
ALok170 wrote:
Dear all, I have a question about using the function 'annFUN.db' in topGO. for which i have converted my gene symbols to probe id (by using annotation package hgu133plus2) and used the function GOdata <- new("topGOdata", ontology = "MF", allGenes = geneList,geneSel = myInterestedGenes,description = "GO analysis of my data.", annot = annFUN.db, affyLib = affyLib) to create the GOdata object and find enriched GO terms. Is there a direct way to find enriched GO terms by using the gene symbols without converting them to probe Id's. Thanks in advance! ALok -- Ph.D scholar Centre of Computational Biology and Bioinformatics School of Information Technology JNU New Delhi [[alternative HTML version deleted]]
ADD COMMENTlink modified 10.3 years ago by Joern Toedling720 • written 10.3 years ago by ALok170
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gravatar for Joern Toedling
10.3 years ago by
Joern Toedling720 wrote:
Hi ALok, you could use the function 'annFUN.gene2GO' instead. Then you have to supply a list that contains the GO identifiers mapped to each gene, which, for example, you can create using the biomaRt package. Here's an example: - suppose we have a list "mm9.gene2GO", which maps Ensembl gene identifiers to GO identifiers: head(mm9.gene2GO) $ENSMUSG00000000001 [1] "GO:0003924" "GO:0005515" "GO:0005737" "GO:0005794" "GO:0005834" [6] "GO:0007186" $ENSMUSG00000000003 [1] "GO:0005549" $ENSMUSG00000000049 [1] "GO:0005615" "GO:0030193" ... - we have a vector of genes of interest: selGenes <- c("ENSMUSG00000000003","ENSMUSG00000000049") - then the way to find GO identifiers enriched for these genes of interest is like this: inGenes <- factor(as.integer(names(mm9.gene2GO) %in% selGenes)) names(inGenes) <- names(mm9.gene2GO) GOdata <- new("topGOdata", ontology="BP", allGenes=inGenes, annot=annFUN.gene2GO, gene2GO=mm9.gene2GO) ... See the topGO vignette for more details on these steps. Hope this helps, Joern ALok wrote: > Dear all, > > I have a question about using the function 'annFUN.db' in topGO. for which i > have converted my gene symbols to probe id (by using annotation package > hgu133plus2) and used the function > > GOdata <- new("topGOdata", ontology = "MF", allGenes = geneList,geneSel = > myInterestedGenes,description = "GO analysis of my data.", annot = > annFUN.db, affyLib = affyLib) > to create the GOdata object and find enriched GO > terms. > > Is there a direct way to find enriched GO terms by using the gene symbols > without converting them to probe Id's. > > Thanks in advance! > ALok >
ADD COMMENTlink written 10.3 years ago by Joern Toedling720
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