Displaying 5 results from an estimated 5 matches for "usemart".
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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...
2007 Jan 26
0
[BioC] problem with biomaRt getHomolog function
....9.15) to do getHomolog queries. A recent change in the
BioMart suite enables the biomaRt package to retrieve both the id you
use to query and the ids in the result of the query.
Here's an example:
rat.entrezgene.ID=c("24842","83502","24205")
mouse.mart <- useMart("ensembl","mmusculus_gene_ensembl")
rat.mart<- useMart("ensembl", "rnorvegicus_gene_ensembl")
mouse.homolog<-getHomolog(id =rat.entrezgene.ID, from.mart =
rat.mart,from.type = "entrezgene",to.type="entrezgene",
to.mart=mouse.mart)...
2009 Jun 16
1
Error using getBM() to query BioMart archives
...within a specific
chromosomal region using biomart. When using the current biomart
database I'm able to do this without issue. However, I need to use
build 36 of the mouse genome which was last included in ensembl mart
46. I selected this mart and the mouse dataset as follows:
mart<-useMart(biomart="ensembl_mart_46", host="www.biomart.org",
path="/biomart/martservice", port=80, archive=TRUE)
mart<-useDataset("mmusculus_gene_ensembl", mart=mart)
I'm able to list the available attributes and filters just fine, but
when I attempt to ac...
2007 Feb 05
3
RSNPper SNPinfo and making it handle a vector
If I run an analysis which generates statistical tests on many SNPs I would
naturally want to get more details on the most significant SNPs. Directly
from within R one can get the information by loading RSNPer (from
Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately,
the command cannot handle a vector and therefore only wants to do one at a
time.
I tried the lapply and
2010 May 28
1
why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
...oblem 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"
[5] "ENST...