search for: getsequence

Hi !  Facing problem with " getSequence" commend .  when only biomaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq...

Hi, I can run the code some days ago . But cant run now.  Problem 1: Output is ok ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl)  Output :                                                                                                5utr  entrezgene                                                                ...

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 erro...

...ges(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'biomaRt' had non-zero exit status > > library(biomaRt) Error in library(biomaRt) : there is no package called 'biomaRt' > ?getBM No matches for "getBM" have been found > ?getSequence No matches for "getSequence" have been found tutti i telefonini TIM! [[alternative HTML version deleted]]

...the slot socket for objects of class seqAcnucWeb: this slot is now deleted. As a consequence, the argument socket in function as.SeqAcnucWeb() has been removed and there is now a new argument socket = "auto" in functions getAnnot(), getFrag(), geyKeyword(), getLocation(), and getSequence(). The default value "auto" means that the details of the socket connection are taken automatically when necessary from the last opened bank. The size of local lists of sequences is reduced by about a third now as compared to the previous version. o New dataset m16j and waterabs...

...the slot socket for objects of class seqAcnucWeb: this slot is now deleted. As a consequence, the argument socket in function as.SeqAcnucWeb() has been removed and there is now a new argument socket = "auto" in functions getAnnot(), getFrag(), geyKeyword(), getLocation(), and getSequence(). The default value "auto" means that the details of the socket connection are taken automatically when necessary from the last opened bank. The size of local lists of sequences is reduced by about a third now as compared to the previous version. o New dataset m16j and waterabs...

...rary("kernlab") >>> >> >> >> > str(mars500_1_df) >> 'data.frame': 256 obs. of 501 variables: >> All of which are factors with 4 levels >> >> >> testSeq_fa=read.fasta("temp1.fasta") >>> testSeq_seq=t(getSequence(testSeq_fa)) >>> testSeq_df=as.data.frame(testSeq_seq,stringsAsFactors=FALSE) >>> testSeq_df = cbind(Class="-",testSeq_df) >>> testSeq_df = data.frame(lapply(testSeq_df,factor)) >>> >> > str(testSeq_df) >> 'data.frame': 20 obs....

...more compatible with glimmer 3.0 outputs. The function has gained a new argument glimmer.version defaulting to 3, but the value 2 is still functional for backward compatibility with old glimmer outputs. o As pointed by Lionel Guy there was no default value for the as.string argument in the getSequence.SeqFastadna(). A default FALSE value is now present for backward compatibility with older code. o New utility vectorized function stresc() to escape LaTeX special characters present in a string. o New low level function readsmj() available. o A new function readfirstrec() to get the record...

...more compatible with glimmer 3.0 outputs. The function has gained a new argument glimmer.version defaulting to 3, but the value 2 is still functional for backward compatibility with old glimmer outputs. o As pointed by Lionel Guy there was no default value for the as.string argument in the getSequence.SeqFastadna(). A default FALSE value is now present for backward compatibility with older code. o New utility vectorized function stresc() to escape LaTeX special characters present in a string. o New low level function readsmj() available. o A new function readfirstrec() to get the record...

...uot; [1933] "ENST00000272190" "ENST00000252268" "ENST00000337907" "ENST00000377464" [1937] "ENST00000400907" "ENST00000400908" "ENST00000440864" "ENST00000309042" [1941] "ENST00000254325" > genes_seq <- getSequence (id=genes_map[,"ensembl_transcript_id"],type="ensembl_transcript_id", + seqType="3utr",mart=hmart) Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is tempor...