Question: use BiomartGeneRegionTrack with the dataset grch37.ensembl.org
0
gravatar for Tiphaine Martin
4.8 years ago by
France
Tiphaine Martin40 wrote:

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

 

biomart gviz ensembl • 1.4k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Tiphaine Martin40
Answer: use BiomartGeneRegionTrack with the dataset grch37.ensembl.org
0
gravatar for Tiphaine Martin
4.8 years ago by
France
Tiphaine Martin40 wrote:

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

ADD COMMENTlink written 4.8 years ago by Tiphaine Martin40
Answer: use BiomartGeneRegionTrack with the dataset grch37.ensembl.org
0
gravatar for Tiphaine Martin
4.8 years ago by
France
Tiphaine Martin40 wrote:

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

ADD COMMENTlink written 4.8 years ago by Tiphaine Martin40
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