VariantAnnotation::locateVariants error coming from XVector
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Entering edit mode
Vivek.b ▴ 100
@vivekb-7661
Last seen 2.2 years ago
Germany

Hi all

I have been getting the following error today on the files which worked fine yesterday : 

Error: subscript is a NSBS object that is incompatible with the current subsetting operation

Happened after I updated some bioconductor packages (don't remember which ones)

 

Reproducible example:

 

library("TxDb.Dmelanogaster.UCSC.dm6.ensGene")

seqlevelsStyle(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "ENSEMBL"

tss <- rtracklayer::import.bed(url("https://bit.ly/2J0rIbj"))

VariantAnnotation::locateVariants(
        query = tss,
        subject = TxDb.Dmelanogaster.UCSC.dm6.ensGene,
        VariantAnnotation::AllVariants(promoter = VariantAnnotation::PromoterVariants(
            upstream = 500, downstream = 0
            )) )

 

SessionInfo:

 

R version 3.5.0 (2018-04-23)

Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /package/R-3.5.0/lib64/R/lib/libRblas.so
LAPACK: /package/R-3.5.0/lib64/R/lib/libRlapack.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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1
[2] GenomicFeatures_1.32.0                   
[3] AnnotationDbi_1.42.1                     
[4] Biobase_2.40.0                           
[5] GenomicRanges_1.32.3                     
[6] GenomeInfoDb_1.16.0                      
[7] IRanges_2.15.13                          
[8] S4Vectors_0.19.6                         
[9] BiocGenerics_0.26.0                      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17                compiler_3.5.0             
 [3] XVector_0.20.0              prettyunits_1.0.2          
 [5] bitops_1.0-6                tools_3.5.0                
 [7] progress_1.1.2              zlibbioc_1.26.0            
 [9] biomaRt_2.36.0              digest_0.6.15              
[11] bit_1.1-13                  BSgenome_1.48.0            
[13] lattice_0.20-35             RSQLite_2.1.1              
[15] memoise_1.1.0               pkgconfig_2.0.1            
[17] Matrix_1.2-14               DelayedArray_0.6.0         
[19] DBI_1.0.0                   GenomeInfoDbData_1.1.0     
[21] rtracklayer_1.40.2          stringr_1.3.1              
[23] httr_1.3.1                  Biostrings_2.48.0          
[25] grid_3.5.0                  bit64_0.9-7                
[27] R6_2.2.2                    XML_3.98-1.11              
[29] BiocParallel_1.15.5         blob_1.1.1                 
[31] magrittr_1.5                Rsamtools_1.32.0           
[33] matrixStats_0.53.1          GenomicAlignments_1.16.0   
[35] assertthat_0.2.0            SummarizedExperiment_1.10.1
[37] stringi_1.2.2               RCurl_1.95-4.10            
[39] VariantAnnotation_1.27.0

 

Any idea?

variantannotation xvector iranges • 709 views
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Entering edit mode
Vivek.b ▴ 100
@vivekb-7661
Last seen 2.2 years ago
Germany

All right problem solved..!

The update of S4Vectors from 0.17 to 0.19 (from GitHub) caused VariantAnnotation functions to break. Downgrading (using biocLite) solved it.

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I believe the changes in S4Vectors were reverted so you could use the latest versions of all packages now. 

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