Displaying 3 results from an estimated 3 matches for "ensembl_transcript_id".
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...
2010 May 28
1
why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
...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"
[5] "ENST00000381588" "ENST00000399762" "ENST00000270357" "ENST00000283646"
[9] "ENST00000314915" "ENST000003566...
2009 Jul 17
0
How to prpare the input data to writeFASTA ? Examples of CharacterToFASTArecords ...
...ion and sequnce in separate variables ... I do not know how to use it.
zz <- file (filname,"w")
write(miRNA.rec, zz, append = FALSE)
write(miRNA.seq,zz, append = TRUE)
#
geneDesc <- paste (">",gene.id, "|", gene.map[i,"ensembl_transcript_id"], sep="")
geneSeq <- gene.seq[i,"3utr"]
gene.string <- list(desc=geneDesc, seq=geneSeq)
writeFASTA (gene.string, zz)
Thank you in advance for your help.
Maura
tutti i telefonini TIM!
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