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Question: warning in makeTxDbFromGFF
0
gravatar for layal8785
19 months ago by
layal87850
layal87850 wrote:

The warning in creating TxDb:

gtffile <- file.path("PATH/Mus_musculus.GRCm38.86.gtf")

txdb <- makeTxDbFromGFF(gtffile, format="gtf")

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular
2: Named parameters not used in query: internal_id, name, type, chrom, strand, start, end
3: Named parameters not used in query: internal_id, name, chrom, strand, start, end
4: Named parameters not used in query: internal_id, name, chrom, strand, start, end
5: Named parameters not used in query: internal_tx_id, exon_rank, internal_exon_id, internal_cds_id
6: Named parameters not used in query: gene_id, internal_tx_id 

 

It doesn't change if I add the other arguments as "dbxrefTag= "GeneName" " or "circ_seqs=character()"

of course I insert the correct path, so PATH is the full path where the gtf file exists:

ADD COMMENTlink modified 19 months ago by James W. MacDonald48k • written 19 months ago by layal87850
0
gravatar for James W. MacDonald
19 months ago by
United States
James W. MacDonald48k wrote:

Those are just warnings that you can safely ignore. They will go away when we release the new version of GenomicFeatures in April.

ADD COMMENTlink written 19 months ago by James W. MacDonald48k
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