[BioC] GenomeGraphs/biomaRt/getBM on older genome builds

[Mark Robinson]

Hi all.

I would like to use GenomeGraphs (specifically, a "GeneRegion" object  
plotted with gdPlot()) ... but I have coordinates from an older genome  
build.  When I try to access the older Ensembl mart, I get an error in  
getBM().

Is this even possible?  I would be delighted if it is.  Of course, it  
does give a warning (see below) that some biomaRt functions will not  
work, so perhaps this is futile.  Is there another alternative?

My commands:

--------
library(GenomeGraphs)

mart <- useMart(biomart="ensembl", dataset="mmusculus_gene_ensembl")
ds <- listDatasets(mart)
ds[grep("mus",ds$desc),]

# RPLP1 on mm8 (i.e. not recent) build
# this will run, but obviously won't find my gene
gr <- new("GeneRegion", chromosome = "9",
                    start = 61711290, end = 61712548, strand="-",  
biomart = mart)

print(gr)

# try the archived version
ensembl46 <- useMart(biomart="ensembl_mart_46",  
dataset="mmusculus_gene_ensembl", archive=TRUE)
ds46 <- listDatasets(ensembl46)
ds46[grep("mus",ds46$desc),]

gr46 <- new("GeneRegion", chromosome = "9",
                    start = 61711290, end = 61712548, strand="-",  
biomart = ensembl46)
--------

My output:

 > library(GenomeGraphs)
Loading required package: biomaRt
Loading required package: grid
 >
 > mart=useMart(biomart="ensembl", dataset="mmusculus_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
 > ds <- listDatasets(mart)
 > ds[grep("mus",ds$desc),]
                   dataset                  description version
43 mmusculus_gene_ensembl Mus musculus genes (NCBIM37) NCBIM37
 >
 > # RPLP1 on mm8 (i.e. not recent) build
 > # this will run, but obviously won't find my gene
 > gr <- new("GeneRegion", chromosome = "9",
+                    start = 61711290, end = 61712548, strand="-",  
biomart = mart)
 >
 > print(gr)
Object of class 'GeneRegion':
  Start:61709290
  End:61714548
  Chromosome: 9
  Exons in Ensembl:
    ensembl_gene_id ensembl_transcript_id ensembl_exon_id  
exon_chrom_start
NA            <NA>                  <NA>            <NA>              
<NA>
    exon_chrom_end rank strand biotype
NA           <NA> <NA>   <NA>    <NA>

  There are 0 more rows>
 >
 > # try the archived version
 > ensembl46=useMart(biomart="ensembl_mart_46",  
dataset="mmusculus_gene_ensembl", archive=TRUE)
Checking attributes ... ok
Checking filters ... ok
Warning messages:
1: In bmAttrFilt("attributes", mart) :
   biomaRt warning: looks like we're connecting to an older version of  
BioMart suite. Some biomaRt functions might not work.
2: In bmAttrFilt("filters", mart) :
   biomaRt warning: looks like we're connecting to an older version of  
BioMart suite. Some biomaRt functions might not work.
 > ds46 <- listDatasets(ensembl46)
 > ds46[grep("mus",ds46$desc),]
                   dataset                  description version
34 mmusculus_gene_ensembl Mus musculus genes (NCBIM36) NCBIM36
 >
 > gr46 <- new("GeneRegion", chromosome = "9",
+                    start = 61711290, end = 61712548, strand="-",  
biomart = ensembl46)
Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id",  
"ensembl_exon_id",  :
   Invalid attribute(s): ensembl_exon_id
Please use the function 'listAttributes' to get valid attribute names
 >
 > sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1

locale:
en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GenomeGraphs_1.3.5 biomaRt_2.0.0

loaded via a namespace (and not attached):
[1] RCurl_0.94-1 XML_2.3-0


Thanks,
Mark



------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852