Entering edit mode
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
