use BiomartGeneRegionTrack with the dataset grch37.ensembl.org
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@tiphaine-martin-6416
Last seen 3.7 years ago
France

Hi Florian,

 

Ensembl change their schema for Gchr37.

I have an error that I don't figure out if the error come from Gviz or the schema of ENSEMBL.

 

chr <- "2"
start <- 38290160
end <- 38303219
gen <- "hg19"
strand <- "*"
martENSEMBL=useMart(host='grch37.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL',
                        dataset='hsapiens_gene_ensembl')

ens_ENSEMBL <- getBM(c("ensembl_gene_id","external_gene_name"),
                       filters = c("chromosome_name","start","end"),
                     values = list(chr, start, end), mart=martENSEMBL)

I have a list of genes

 

but when I am doing  

biomTrack <- BiomartGeneRegionTrack(genome = gen, biomart=martENSEMBL,
                                     chromosome = chr, start = start,
                                     end = end,  name = "ENSEMBL",
                                     groupAnnotation = "group",
                                     just.group = "above",
                                     fontcolor="black",showId=showId,size=2)

I have this error message

Error in getBM(as.vector(featureMap), filters = filterNames, values = filterValues,  :
  Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed

but if I am doing the same on a older version of ENSEMBL or the last version, I don't have this error message. Of course, I don't have the same plot because the sequences of genome change.

martENSEMBL=useMart(host='oct2012.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL',
                         dataset='hsapiens_gene_ensembl')

   fm <- Gviz:::.getBMFeatureMap()
 fm["symbol"] <- "external_gene_id"

biomTrack <- BiomartGeneRegionTrack(genome = gen, featureMap=fm, biomart=martENSEMBL,
                                         chromosome = chr, start = start,
                                         end = end,  name = "ENSEMBL",
                                        fontcolor="black",showId=TRUE,size=2)
 plotTracks(biomTrack)

or

biomTrack <- BiomartGeneRegionTrack(genome = gen,
                                         chromosome = chr, start = start,
                                         end = end,  name = "ENSEMBL",
                                        fontcolor="black",showId=TRUE,size=2)

plotTracks(biomTrack)

 

Could you help me to use the version of ENSEMBL mart " grch37.ensembl.org" with Gviz ?

 

Regards,

Tiphaine

> sessionInfo()
R Under development (unstable) (2014-12-17 r67184)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
[1] XVector_0.7.3         biomaRt_2.23.5        Gviz_1.11.4          
[4] GenomicRanges_1.19.23 GenomeInfoDb_1.3.9    IRanges_2.1.33       
[7] S4Vectors_0.5.14      BiocGenerics_0.13.3  

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3           AnnotationDbi_1.29.11    
 [3] base64enc_0.1-2           BatchJobs_1.5            
 [5] BBmisc_1.8                Biobase_2.27.0           
 [7] BiocParallel_1.1.9        Biostrings_2.35.7        
 [9] biovizBase_1.15.1         bitops_1.0-6             
[11] brew_1.0-6                BSgenome_1.35.10         
[13] checkmate_1.5.1           cluster_1.15.3           
[15] codetools_0.2-9           colorspace_1.2-4         
[17] DBI_0.3.1                 dichromat_2.0-0          
[19] digest_0.6.6              fail_1.2                 
[21] foreach_1.4.2             foreign_0.8-61           
[23] Formula_1.1-2             GenomicAlignments_1.3.19
[25] GenomicFeatures_1.19.8    Hmisc_3.14-6             
[27] iterators_1.0.7           lattice_0.20-29          
[29] latticeExtra_0.6-26       matrixStats_0.12.2       
[31] munsell_0.4.2             nnet_7.3-8               
[33] plyr_1.8.1                RColorBrewer_1.1-2       
[35] Rcpp_0.11.3               RCurl_1.95-4.5           
[37] R.methodsS3_1.6.1         rpart_4.1-8              
[39] Rsamtools_1.19.18         RSQLite_1.0.0            
[41] rtracklayer_1.27.6        scales_0.2.4             
[43] sendmailR_1.2-1           splines_3.2.0            
[45] stringr_0.6.2             survival_2.37-7          
[47] tools_3.2.0               VariantAnnotation_1.13.20
[49] XML_3.98-1.1              zlibbioc_1.13.0

 

gviz ensembl biomart • 1.8k views
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Entering edit mode
@tiphaine-martin-6416
Last seen 3.7 years ago
France

I find where the error comes from.

In the section “Structures” of attributes of ENSEMBL mart,  the version GRCh37.p13 does not have the attribute "Associated Gene Name” , but the version GRCh38 do have it.
Previously, GRCh37 have the attribute "Associated Gene Name” In the section “Structures”.

I don't know if  the correction should be in Gviz or ENSEMBL

Tiphaine

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Entering edit mode
@tiphaine-martin-6416
Last seen 3.7 years ago
France

The Ensembl mart for GChr37 was changed.

the missing "Associated Gene Name" attribute in the structure, sequence, variation and homolog pages of the GRCh37 ensembl mart (http://grch37.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id|hsapiens_gene_ensembl.default.feature_page.external_gene_name|hsapiens_gene_ensembl.default.feature_page.external_gene_db&FILTERS=&VISIBLEPANEL=resultspanel).

So everything works again.

Thank Thomas.

 

Tipahine

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