search for: 3utr

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...

I executed the following lines several times from a script as well as pasting them in an R shell. Systematically biomaRt is failing. 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', d...

...t;, header=TRUE, sep="\t", fill=TRUE, na.strings="NA", comment.char="", stringsAsFactors = FALSE) However, I encounter troubles in interpreting some "\t" separator.. A column displays \t\t\t\t characters fusioning consecutive columns and rows? see: "Body;3UTR\t\t\t\t\t\t\t\t\t\n3\tcg00000109\t59755374\t59755374\t0.8353283\t2657\t7\t7\t122.8385\t241.5193\t354\t2303\t0.00\t0.005" Is there any way to deal with such problem? Kind Regards Sandrine -- Sandrine Imbeaud INSERM, UMR U-674, IUH Université Paris Descartes Génomique Fonctionnelle des tum...

...le (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! [[alternative HTML version deleted]]