How to include the metadata when we build the txDb object?
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4 weeks ago
qwesxadzc9 • 0

Hello everyone,

I am using the makeTxDbFromGFF function from GenomicFeatures to convert a gff3 file that is downloaded from Gencode to a TxDb object. But I find out with this function all the additional information that provides by Gencode was missing. For example, transcript_support_level, transcript_type and so on.

I was wondering is there a proper way to keep all these information when we make a TxDb object from gff3 file? Thank you in advance.

Best regards, Y.Zhou

txdb r • 204 views
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Did you see the makeTxDb function documentation ? You can pass a metadata data frame with makeTxDbFromGFF which gets handed down to makeTxDbFromGRanges and then makeTxDb

metadata:

2-column data frame containing meta information about this set of transcripts like organism, genome, UCSC table, etc... The names of the columns must be "name" and "value" and their type must be character.

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Hey Carambakaracho, thanks for your answer. I know we can do it like that, but we will need to make the meta data as a 2 column data frame ourself. I was wondering whether there is a more elegent way to do that : )

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