Question: How to see into a txdb object?
1
gravatar for Parham
4.5 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

Hi, 

I make txdb as below. I would like to see what is inside this object and to know what information do I have. How can I do it? head() gives an error.

> txdb <- makeTranscriptDbFromBiomart(biomart="fungal_mart", dataset="spombe_eg_gene", host="fungi.ensembl.org")\
> head(txdb)
Error in x[seq_len(n)] : object of type 'S4' is not subsettable
txdb • 3.3k views
ADD COMMENTlink modified 4.5 years ago by Devon Ryan89k • written 4.5 years ago by Parham1.4k
6
gravatar for Devon Ryan
4.5 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Just typing txdb will give you basic information about the object. A TranscriptDb is essentially a database, so there's no simple way to see what's in it, since that has no meaning. If you want to see what sorts of things you can select from it, then columns(txdb) is pretty informative. If you're familiar with SQL, you can treat it as an SQL database and select(txdb, keys=some_vector, columns=...). Aside from that, you likely just want the standard functions like transcript(), exon() and so on.

Edit: BTW, if you really want to see everything, then select(txdb, columns=columns(txdb), keys=keys(txdb), keytype=c("GENEID")) should do it.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Devon Ryan89k
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