Trouble while concatenating VRanges object ()
Entering edit mode
Last seen 3.8 years ago

Hi everyone, 

I am using the very interesting SomaticSignatures package, and I have an Error now for which I didn't manage to find an answer on this support site. 

I managed to concatenate some VRanges objects to one, and so all the functions are working wonderfully to get some signatures, but for others objects I do not manage to build the vector and the results are two different kind of Errors (depending on the VRanges objects I try to concatenate). 

Here is the code : 

1) "vr_caf34" is one of the VCF file transformed in VRange, so you see the method I used :

> vr_caf34 = readVcfAsVRanges("C:/path/to/vcf_CDS/CAFSARC34.pPDGFRBCDS.torrent.snpEff.vcf", "GenomeA")
> mcols(vr_caf34)$sample = "caf34"
> vr_CDS = c(vr_caf32, vr_caf33, vr_caf34, vr_caf40, vr_caf41, vr_caf46, vr_caf50, vr_caf60, vr_caf62, vr_caf63, vr_caf64)
> vr_CDS
VRanges object with 1705 ranges and 63 metadata columns:
Error: subscript is a NSBS object that is incompatible with the current subsetting operation


2) Trying to combine other VRanges objects (from other VCF files), I get : 

> vr_caf2 = readVcfAsVRanges("C:/path/to/vcf_PAPBKIT/CAFSARC-2.pPAPBKIT.torrent.snpEff.vcf", "GenomeA")
> mcols(vr_caf2)$sample = "caf2"
> vr_PAPBKIT = c(vr_caf2, vr_caf7, vr_caf9, vr_caf10, vr_caf11, vr_caf15, vr_caf16, vr_caf18)
Error in combine_CompressedList_objects(class(x), objects, use.names = FALSE,  : 
  the objects to combine must be CompressedList objects (or NULLs)


I tried several times today, but I can't find a solution. My R version is uptodate and so are the packages I am using (I think...). 

Thank you so much for your help !

Cheers, Guillaume 

somaticsignatures somaticsignatures package readvcfasvranges vranges • 1.6k views
Entering edit mode

This may be caused by the content of your VCF files, but without knowing how they look like, it will be hard to provide a solution. In order to narrow down the problem, can you please:

  • Try to simplify the example: Do you need all 8 VCFs to reproduce the error? Does it happen with any combination of two VCFs?
  • Is there a way you can share the problematic data? If not, have you had a look at the content of the VCF files and checked if there is anything special about some of them?
  • Can you please provide the output of your sessionInfo?
Entering edit mode
Last seen 3.8 years ago

Dear Julian, 

Thank you so much for taking the time to answer my questions.

To answer yours :

  • The VCFs are not very different when I look at them, but indeed the error is reproduced when I try to combine VCFs from different experiments (but same sequencer, same tumor, same genes analyzed, same variant caller,...). When I combine VCFs generated from one experiment, it's seems to be OK. 
  • If you agree to have a look by yourself, I can send you two problematic VCFs. 
  • Here is the output of the sessionInfo : 
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

[1] LC_COLLATE=French_Belgium.1252  LC_CTYPE=French_Belgium.1252    LC_MONETARY=French_Belgium.1252 LC_NUMERIC=C                    LC_TIME=French_Belgium.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SomaticSignatures_2.12.1   NMF_0.20.6                 cluster_2.0.6              rngtools_1.2.4             pkgmaker_0.22              registry_0.3              
 [7] VariantAnnotation_1.22.3   Rsamtools_1.28.0           Biostrings_2.44.2          XVector_0.16.0             SummarizedExperiment_1.6.3 DelayedArray_0.2.7        
[13] matrixStats_0.52.2         Biobase_2.36.2             GenomicRanges_1.28.4       GenomeInfoDb_1.12.2        IRanges_2.10.2             S4Vectors_0.14.3          
[19] BiocGenerics_0.22.0       

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.8.0            bitops_1.0-6                  bit64_0.9-7                   doParallel_1.0.10             RColorBrewer_1.1-2           
 [6] httr_1.2.1                    tools_3.4.1                   backports_1.1.0               R6_2.2.2                      rpart_4.1-11                 
[11] Hmisc_4.0-3                   DBI_0.7                       lazyeval_0.2.0                colorspace_1.3-2              nnet_7.3-12                  
[16] gridExtra_2.2.1               GGally_1.3.2                  curl_2.8.1                    bit_1.1-12                    compiler_3.4.1               
[21] graph_1.54.0                  htmlTable_1.9                 rtracklayer_1.36.4            ggbio_1.24.1                  scales_0.4.1                 
[26] checkmate_1.8.3               proxy_0.4-17                  RBGL_1.52.0                   stringr_1.2.0                 digest_0.6.12                
[31] foreign_0.8-69                base64enc_0.1-3               dichromat_2.0-0               htmltools_0.3.6               ensembldb_2.0.3              
[36] BSgenome_1.44.0               htmlwidgets_0.9               rlang_0.1.1                   RSQLite_2.0                   BiocInstaller_1.26.0         
[41] shiny_1.0.3                   BiocParallel_1.10.1           acepack_1.4.1                 RCurl_1.95-4.8                magrittr_1.5                 
[46] GenomeInfoDbData_0.99.0       Formula_1.2-2                 Matrix_1.2-10                 Rcpp_0.12.12                  munsell_0.4.3                
[51] stringi_1.1.5                 yaml_2.1.14                   zlibbioc_1.22.0               plyr_1.8.4                    AnnotationHub_2.8.2          
[56] grid_3.4.1                    blob_1.1.0                    lattice_0.20-35               splines_3.4.1                 GenomicFeatures_1.28.4       
[61] knitr_1.16                    reshape2_1.4.2                codetools_0.2-15              biomaRt_2.32.1                XML_3.98-1.9                 
[66] biovizBase_1.24.0             latticeExtra_0.6-28           pcaMethods_1.68.0             data.table_1.10.4             httpuv_1.3.5                 
[71] foreach_1.4.3                 gtable_0.2.0                  reshape_0.8.6                 ggplot2_2.2.1                 gridBase_0.4-7               
[76] mime_0.5                      xtable_1.8-2                  AnnotationFilter_1.0.0        survival_2.41-3               OrganismDbi_1.18.0           
[81] tibble_1.3.3                  iterators_1.0.8               GenomicAlignments_1.12.1      AnnotationDbi_1.38.2          memoise_1.1.0                
[86] interactiveDisplayBase_1.14.0


Once again, thanks a lot. 

Have a good week-end. 



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