BioMart webservice returned an invalid result
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0
Entering edit mode
adrian86 • 0
@adrian86-22785
Last seen 21 months ago
  • I'm using "hg19" and so I'm unable to switch mirrors in the useEnsembl() function as the previously questions inform. The actual code of reproducible example would be:
library(Gviz)
library(biomaRt)
m37 <- useEnsembl(biomart = "ensembl", GRCh = 37, mirror = "eastusa", dataset = "hsapiens_gene_ensembl")
TET2 <- c( 4, 106067032 - 5000, 106200973 + 5000)
btrack <- Gviz::BiomartGeneRegionTrack(genome = "hg19", biomart = m37,
                    chromosome = TET2[1], start = TET2[2], end = TET2[3],
                    showId = FALSE, geneSymbols = FALSE,
                    rotate.title = TRUE, col.line = NULL,
                    col = "orange", fill = "orange",
                    filters = list(biotype = "protein_coding"),
                    collapseTranscripts = FALSE)
  • Whole console output with traceback() and sessionInfo():
> m37 <- useEnsembl(biomart = "ensembl", GRCh = 37, mirror = "eastusa", dataset = "hsapiens_gene_ensembl")
Warning message:
In useEnsembl(biomart = "ensembl", GRCh = 37, mirror = "eastusa",  :
  version or GRCh arguments can not be used together with the mirror argument.', 
                'We will ignore the mirror argument and connect to main Ensembl site.
> TET2 <- c( 4, 106067032 - 5000, 106200973 + 5000)
> btrack <- Gviz::BiomartGeneRegionTrack(genome = "hg19", biomart = m37,
+                     chromosome = TET2[1], start = TET2[2], end = TET2[3],
+                     showId = FALSE, geneSymbols = FALSE,
+                     rotate.title = TRUE, col.line = NULL,
+                     col = "orange", fill = "orange",
+                     filters = list(biotype = "protein_coding"),
+                     collapseTranscripts = FALSE)
Error in getBM(as.vector(featureMap), filters = names(filterValues), values = filterValues,  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 
Please report this on the support site at http://support.bioconductor.org
> traceback()
9: stop("The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. \nPlease report this on the support site at http://support.bioconductor.org")
8: getBM(as.vector(featureMap), filters = names(filterValues), values = filterValues, 
       bmHeader = FALSE, mart = object@biomart, uniqueRows = TRUE)
7: .fetchBMData(bmtrack, chromosome, staged)
6: .cacheMartData(.Object, chromosome, staged)
5: .local(.Object, ...)
4: initialize(value, ...)
3: initialize(value, ...)
2: new("BiomartGeneRegionTrack", start = start, end = end, chromosome = chromosome, 
       strand = strand, biomart = biomart, name = name, genome = genome, 
       stacking = stacking, filter = filters, featureMap = featureMap, 
       symbol = symbol, gene = gene, transcript = transcript, entrez = entrez, 
       ...)
1: Gviz::BiomartGeneRegionTrack(genome = "hg19", biomart = m37, 
       chromosome = TET2[1], start = TET2[2], end = TET2[3], showId = FALSE, 
       geneSymbols = FALSE, rotate.title = TRUE, col.line = NULL, 
       col = "orange", fill = "orange", filters = list(biotype = "protein_coding"), 
       collapseTranscripts = FALSE)
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS/LAPACK: /home/username/.conda/envs/jupy/lib/libopenblasp-r0.3.7.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.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] biomaRt_2.40.3       Gviz_1.28.0          GenomicRanges_1.36.0
[4] GenomeInfoDb_1.20.0  IRanges_2.18.2       S4Vectors_0.22.0    
[7] BiocGenerics_0.30.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.44.0              httr_1.4.1                 
 [3] bit64_0.9-7                 splines_3.6.1              
 [5] Formula_1.2-3               assertthat_0.2.1           
 [7] latticeExtra_0.6-28         blob_1.2.0                 
 [9] BSgenome_1.52.0             GenomeInfoDbData_1.2.1     
[11] Rsamtools_2.0.0             progress_1.2.2             
[13] pillar_1.4.2                RSQLite_2.1.2              
[15] backports_1.1.4             lattice_0.20-38            
[17] biovizBase_1.32.0           glue_1.3.1                 
[19] digest_0.6.20               RColorBrewer_1.1-2         
[21] XVector_0.24.0              checkmate_1.9.4            
[23] colorspace_1.4-1            htmltools_0.3.6            
[25] Matrix_1.2-17               XML_3.98-1.20              
[27] pkgconfig_2.0.2             zlibbioc_1.30.0            
[29] purrr_0.3.2                 scales_1.0.0               
[31] BiocParallel_1.18.0         tibble_2.1.3               
[33] htmlTable_1.13.2            AnnotationFilter_1.8.0     
[35] ggplot2_3.2.1               GenomicFeatures_1.36.4     
[37] SummarizedExperiment_1.14.0 nnet_7.3-12                
[39] lazyeval_0.2.2              survival_2.44-1.1          
[41] magrittr_1.5                crayon_1.3.4               
[43] memoise_1.1.0               xml2_1.2.2                 
[45] foreign_0.8-72              data.table_1.12.8          
[47] tools_3.6.1                 prettyunits_1.0.2          
[49] hms_0.5.1                   matrixStats_0.55.0         
[51] stringr_1.4.0               munsell_0.5.0              
[53] cluster_2.1.0               DelayedArray_0.10.0        
[55] ensembldb_2.8.0             AnnotationDbi_1.46.0       
[57] Biostrings_2.52.0           compiler_3.6.1             
[59] rlang_0.4.0                 RCurl_1.95-4.12            
[61] dichromat_2.0-0             rstudioapi_0.10            
[63] VariantAnnotation_1.30.1    htmlwidgets_1.3            
[65] bitops_1.0-6                base64enc_0.1-3            
[67] gtable_0.3.0                curl_4.0                   
[69] DBI_1.0.0                   R6_2.4.0                   
[71] GenomicAlignments_1.20.1    gridExtra_2.3              
[73] knitr_1.24                  dplyr_0.8.3                
[75] rtracklayer_1.44.2          bit_1.1-14                 
[77] zeallot_0.1.0               Hmisc_4.2-0                
[79] ProtGenerics_1.16.0         stringi_1.4.3              
[81] Rcpp_1.0.2                  vctrs_0.2.0                
[83] rpart_4.1-15                acepack_1.4.1              
[85] xfun_0.9                    tidyselect_0.2.5           
> 
  • Now, my actual question would be in regard to what I was looking forward to achive. I tried the Gviz vignette example with built-in geneModel. I want to see that track on TET2 gene (GRCh37 coordinates with 5kbp expansion are present in my code). Is this how I can build a geneModel track?

Thanks in advance.

gviz biomart • 235 views
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Entering edit mode

I've switched to UCSC/ rtracklayer and it works.

TET2.start <- 106067032 - 5000
TET2.end <- 106200973 + 5000

library(rtracklayer)
session <- browserSession()
genome(session) <- "hg19"
trackNames(session)

library(Gviz)
ucscTrack <- UcscTrack(genome = "hg19", track = "ensGene",
                       chromosome = "chr4", strand = "strand",
                       from = TET2.start, to = TET2.end,
                       trackType = "GeneRegionTrack",
                       rstarts = "exonStarts", rends = "exonEnds",
                       gene ="name", symbol = "name2",
                       transcript = "name")

plotTracks(c(ucscTrack), from = TET2.start, to = TET2.end)
ADD REPLY
0
Entering edit mode
Robert Ivanek ▴ 700
@robert-ivanek-5892
Last seen 7 days ago
Switzerland

Hi, There are some changes regarding the GRCh37/hg19 genome in ensembl itself. https://m.ensembl.org/info/website/tutorials/grch37.html

In the Gviz vignette, there is a description how to get the data:

library(Gviz)
library(biomaRt)

bm <- useMart(host="grch37.ensembl.org", 
              biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")

TET2 <- c( 4, 106067032 - 5000, 106200973 + 5000)
biomTrack <- BiomartGeneRegionTrack(genome="hg19", 
                                    chromosome = TET2[1], start = TET2[2], end = TET2[3],
                                    name="ENSEMBL", biomart=bm)

plotTracks(biomTrack)

Best, Robert

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