![]() Make your own NCBI-based OrgDb package > library(AnnotationForge) The downside of doing that, IMO is you are relying on this mapping Ensembl ID -> Gene ID -> Gene symbolĪnd there are often technical reasons for genes to not map from Ensembl to NCBI, so you can lose lots of genes that way. ![]() > z select(ensdb, z, "GENENAME","ENTREZID") # LOCs are just the NCBI Gene ID prepended with a LOC # retrieve records with, e.g., 'object]'ĪH79739 | Ensembl 100 EnsDb for Oncorhynchus mykissĪH80248 | Oncorhynchus_mykiss.Omyk_1.0.ĪH80249 | Oncorhynchus_mykiss.Omyk_1.0.ĪH80250 | Oncorhynchus_mykiss.Omyk_1.0.100.gtf # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # additional mcols(): taxonomyid, genome, description, Two other alternatives are Use the AnnotationHub > library(AnnotationHub) Row.names(diffGenesData)=diffGenesData$gene_idĭiffGenesOutput<-merge(diffGenesNames,diffGenesData,by="row.names")ĭoes anyone have a solution to this problem? #gene_short_name values (and corresponding XLOC_* values) can be retrieved from the CuffGeneSet by using: #Use returned identifiers to create a CuffGeneSet object with all relevant info for given genes #Retrive significant gene IDs (XLOC) with a pre-specified alphaĭiffGeneIDs <- getSig(cuff,level="genes",alpha=0.05) I also tried the following command in the R software cummeRbund package, but the output answers were as LOCs ID. I also read all the relevant biostars content but did not get the required result: I also tried the following sites but it was not successful: I searched repeatedly in section Gene in NCBI, but the results Were obtained as LOCs. Is there any way to convert XLOCs back to Gene symbols? The output of cuffdiff replaced the Gene symbol (official gene symbol) with XLOC's such as: LOC110534079Įxample : LOC110537830 (ID) = mknk1 (Gene symbol) When I did RNA-Seq analysis, the GTF file I used was from NCBI.
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