Entering edit mode
Hello Bioc users,
I am having trouble in finding attribute "mirbase" in the biomaRt
latest ensembl version. I can find it in the ensembl_mart_51 version
but not in the latest version (ENSEMBL GENES 60). Is there any way to
add that attribute so that the latest miRNA coordinates can be
retrieved.
Thank you,
Neel
Here is my session info.
R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
[R.app GUI 1.34 (5589) i386-apple-darwin9.8.0]
biomaRt 2.4.0
> library("biomaRt")
> listMarts()
biomart
version
1 ensembl ENSEMBL GENES
60 (SANGER UK)
2 snp ENSEMBL VARIATION
60 (SANGER UK)
3 functional_genomics ENSEMBL FUNCTIONAL GENOMICS
60 (SANGER UK)
4 vega VEGA
40 (SANGER UK)
> listMarts(archive=TRUE)
biomart version
1 ensembl_mart_51 Ensembl 51
2 snp_mart_51 SNP 51
3 vega_mart_51 Vega 32
4 ensembl_mart_50 Ensembl 50
5 snp_mart_50 SNP 50
6 vega_mart_50 Vega 32
7 ensembl_mart_49 ENSEMBL GENES 49 (SANGER)
> ensembl=useDataset("drerio_gene_ensembl", mart= ensembl)
Checking attributes ... ok
Checking filters ... ok
> filters=listFilters(ensembl)
> filters
name
description
24 with_mirbase
with miRBase ID(s)
25 with_rfamR
with Rfam ID(s)
> attributes = listAttributes(ensembl)
> attributes
# I DO NOT FIND mirbase in this list.
> miRNA = getBM(c("mirbase","ensembl_gene_id","start_position","chromo
some_name"), filters=c("chromosome_name","with_mirbase"), values=
list(13, TRUE), mart = ensembl)
Error in getBM(c("mirbase", "ensembl_gene_id", "start_position",
"chromosome_name"), :
Invalid attribute(s): mirbase
# When I change the database to ensembl_mart_51, mirbase appears.
> ensembl = useMart("ensembl_mart_51", dataset =
"drerio_gene_ensembl",archive=TRUE)
Checking attributes ... ok
Checking filters ... ok
> listAttributes(ensembl)
name
description
34 mirbase
miRBase
Neel Aluru
Postdoctoral Scholar
Biology Department
Woods Hole Oceanographic Institution
Woods Hole, MA 02543
USA
508-289-3607