Displaying 3 results from an estimated 3 matches for "hsapiens_gene_ensembl".
2013 Feb 08
1
Conflict command getSequence {biomaRt} and getSequence {seqinr} !!
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)
but when i have loaded the seqinr, i got problem with same commend .
> mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
> s...
2013 May 07
1
Problem with biomaRt::getSequence.
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
...
2010 May 28
1
why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
...orresponding 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"
[5] "ENST00000381588" "ENST00000399762" "EN...