[BioC] How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures?

[Ying Chen]

Hi guys,

I am new to the GenomicsFeatures package and I am trying to make my own txdb out of TCGA GAF file using the function makeTranscriptDb(transcripts, splicings,genes) in GenomicsFeatures. The manual says that genes is a data frame containing the genes associated to a set of transcripts. I just wonder what format should it be. Will the following work?

 genes <- data.frame(
                   tx_id=c(txid1,txid2, txid3, txid4, txid5, txid6, txid7, txid8, txid9,............),                                                              # first 9 tx_ids for 3 gene_ids are listed
                  gene_id=c(geneid1, geneid1, geneid2, geneid2, geneid2, geneid3, geneid3, geneid3, geneid3,.......))     # first 3 gene_ids are listed

Thanks a lot for the help!

Ying

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