[BioC] problem getting biotype in biomaRt
Elizabeth Purdom
epurdom at stat.berkeley.edu
Fri Jan 9 21:22:09 CET 2009
Hi,
I am trying to pull down information from Ensembl using biomaRt and I
can't get the relevant biotype information (for Human). The old
'biotype' attribute doesn't exist, so what I see is 'gene_biotype' and
'structure_biotype'. I have no idea what the difference is, but I can't
get either one. The error says it's probably an internal error to be
reported, but I also get this when I try to bring down what I think are
incompatible attributes.
Thanks,
Elizabeth
> library(biomaRt)
> mart<-useMart("ensembl",dataset= "hsapiens_gene_ensembl")
Checking attributes and filters ... ok
> martAttr<-listAttributes(mart)
> att<-c("ensembl_gene_id",
+ "ensembl_transcript_id",
+ "ensembl_exon_id",
+ "exon_chrom_start",
+ "exon_chrom_end",
+ "strand",
+ "chromosome_name",
+ "rank",
+ "3_utr_start","3_utr_end",
+ "5_utr_start","5_utr_end"
+ )
> all(att%in%martAttr[,1]) #valid names for the mart
[1] TRUE
#works fine here
> tempGene <-
getBM(att,filter="ensembl_gene_id",value="ENSG00000187634",mart = mart)
#error
> tempGene <-
getBM(c(att,"gene_biotype"),filter="ensembl_gene_id",value="ENSG00000187634",mart
= mart)
V1
1 Query ERROR: caught BioMart::Exception::Usage: Attributes from
multiple attribute pages are not allowed
Error in getBM(c(att, "gene_biotype"), filter = "ensembl_gene_id", value
= "ENSG00000187634", :
Number of columns in the query result doesn't equal number of
attributes in query. This is probably an internal error, please report.
#again an error
> tempGene <-
getBM(c(att,"structure_biotype"),filter="ensembl_gene_id",value="ENSG00000187634",mart
= mart)
V1
1 Query ERROR: caught BioMart::Exception::Usage: Attribute biotype NOT FOUND
Error in getBM(c(att, "structure_biotype"), filter = "ensembl_gene_id", :
Number of columns in the query result doesn't equal number of
attributes in query. This is probably an internal error, please report.
> sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_1.16.0
loaded via a namespace (and not attached):
[1] RCurl_0.93-0 tools_2.8.1 XML_1.99-0
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