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Question: biomaRt have asked me to report this
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gravatar for daniil.sarkisyan
16 months ago by
Sweden
daniil.sarkisyan10 wrote:
Dear biomaRt developers,

Reporting, just as you have asked:

> library(biomaRt)
> mart <- useMart('ENSEMBL_MART_SNP',"hsapiens_snp_som")
> mart.a <- listAttributes(mart)
> attr <- subset(mart.a, grepl("sequences", page))$name
> pdyn <- getBM(
+ attributes = attr,
+ filters = c("chromosomal_region"), values = list(chromosomal_region="20:1968757:2004285"),
+ mart = mart)
                 V1 V2      V3      V4 V5          V6     V7              V8                   V9
1 %COSMIC_MUTATION% 20 1980467 1980467  1  COSM477874 COSMIC COSMIC_MUTATION Phenotype_or_Disease
2 %COSMIC_MUTATION% 20 1980454 1980454  1 COSM1565883 COSMIC COSMIC_MUTATION Phenotype_or_Disease
3 %COSMIC_MUTATION% 20 1980472 1980472  1 COSM1326867 COSMIC COSMIC_MUTATION Phenotype_or_Disease
4 %COSMIC_MUTATION% 20 1980484 1980484  1 COSM3544459 COSMIC COSMIC_MUTATION Phenotype_or_Disease
5 %COSMIC_MUTATION% 20 1980442 1980442  1 COSM3963357 COSMIC COSMIC_MUTATION Phenotype_or_Disease
6 %COSMIC_MUTATION% 20 1980453 1980453  1 COSM1716135 COSMIC COSMIC_MUTATION Phenotype_or_Disease
Error in getBM(attributes = attr, filters = c("chromosomal_region"), values = list(chromosomal_region = "20:1968757:2004285"),  : 
  The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.28.0

loaded via a namespace (and not attached):
 [1] IRanges_2.6.1        parallel_3.3.1       DBI_0.4-1            tools_3.3.1         
 [5] RCurl_1.95-4.8       Biobase_2.32.0       AnnotationDbi_1.34.4 RSQLite_1.0.0       
 [9] S4Vectors_0.10.2     BiocGenerics_0.18.0  stats4_3.3.1         bitops_1.0-6        
[13] XML_3.98-1.4
ADD COMMENTlink written 16 months ago by daniil.sarkisyan10
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