Displaying 2 results from an estimated 2 matches for "hmart".
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smart
2009 Aug 03
3
How to catch an error using try
Sometimes the following function call causes a database exception:
> gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], type="ensembl_transcript_id",
+ seqType="3utr", mart=hmart)
I understand the above function must be called by try to capture the eventual error.
WHat is not clear to me is how to realize that an error has occurred. The on-line documentation
mentions an invisible object of class "try-error".
How shall I test whetehr such object has been created...
2010 May 28
1
why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
...ling.
The problem is to extract the 3UTR sequences corresponding to a vector containing 1941
Ensembl Transcript numbers (some are duplicated ... is this s problem ?)
Please, find the failing instructions in the following including the ENST vector
Any suggestion is welcome. Thank you,
Maura
> hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
Checking attributes ... ok
Checking filters ... ok
> genes_map[,"ensembl_transcript_id"]
[1] "ENST00000262187" "ENST00000296271" "ENST00000346166" "ENST00000381570"...