problems annotating genes using org.Hs.eg.db
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10 months ago
brtawe • 0

I am trying to use org.Hs.eg.db to annotate gene IDs extracted from calling genes on a TxDB as such

genes <- genes(TxDb.Hsapiens.UCSC.hg38.knownGene)
overlaps <-  join_overlap_left_directedmycoords.gr, genes)
gene_result = as(overlaps, "data.frame")


I used this code taken directly from here https://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf

annots <- select(org.Hs.eg.db, keys=gene_result$gene_id, columns=c("SYMBOL","GENENAME"), keytype="ENTREZID")  But I get the following error message Error in UseMethod("select_") : no applicable method for 'select_' applied to an object of class "c('OrgDb', 'AnnotationDb', 'envRefClass', '.environment', 'refClass', 'environment', 'refObject', 'AssayData')"  Any help or an alternate method would be appreciated. R • 949 views ADD COMMENT 0 Entering edit mode What is the output of str(gene_result)? ADD REPLY 0 Entering edit mode It's a data frame made from a GRanges object gene_result = as(overlaps, "data.frame") #convert GRanges object to data frame  problem fixed via other comment, thanks for your help anyway! ADD REPLY 3 Entering edit mode 10 months ago There are a few common packages with the select function, so try to explicitly state the correct namespace so R knows what library to use. annots <- AnnotationDbi::select( org.Hs.eg.db, keys=gene_result$gene_id,
columns=c("SYMBOL","GENENAME"), keytype="ENTREZID"
)

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This fixed it, thanks! I thought this might be the problem since dplyr uses "select" as well. I did not know how to specify functions to packages, this is good knowledge.

I should probably have included all the packages I was using, but the interface here only allows me to add one line of code at a time (or I don't know how to add multiple lines), so I only included what I thought was essential.

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