AnnotationDbi using UCSC annotation

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7.4 years ago

jadepinket ▴ 10

I have used UCSC GTF file to annotate my reads, now I am having trouble doing the following

library("AnnotationDbi") library("org.Hs.eg.db") columns(org.Hs.eg.db)

res$symbol = mapIds(org.Hs.eg.db, keys=row.names(res), column="SYMBOL", keytype="ENSEMBL", multiVals="first") res$entrez = mapIds(org.Hs.eg.db, keys=row.names(res), column="ENTREZID", keytype="ENSEMBL", multiVals="first") res$name = mapIds(org.Hs.eg.db, keys=row.names(res), column="GENENAME", keytype="ENSEMBL", multiVals="first")

my row name does not match any database it looks like this "ENST00000000233.9", "ENST00000000412.7", "ENST00000001008.5", "ENST00000002165.10"

ENSEMBLETRANS has transcripts annotated with ENST######### but .9,.7, .5 at the end is missing. So my row names are not being read by any database. I have tried HomoSapiens and TxDb

Any suggestions on this would be helpful. Thanks

RNA-Seq AnntationDbi UCSC GTF • 2.5k views

ADD COMMENT • link 7.4 years ago by jadepinket ▴ 10

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Entering edit mode

Below is the error I get, any suggestions would be helpful

res$symbol <- mapIds(TxDb.Hsapiens.UCSC.hg38.knownGene, keys=row.names(res), column="CDSNAME", keytype="TXID", multiVals="first")

Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'TXID'. Please use the keys method to see a listing of valid arguments.

ADD REPLY • link 7.4 years ago by jadepinket ▴ 10

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