Question: Trouble while concatenating VRanges object ()
0
gravatar for guillaume.dachy
21 months ago by
Brussels
guillaume.dachy0 wrote:

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 

ADD COMMENTlink modified 20 months ago • written 21 months ago by guillaume.dachy0
1

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?
ADD REPLYlink written 20 months ago by Julian Gehring1.3k
Answer: Trouble while concatenating VRanges object ()
0
gravatar for guillaume.dachy
20 months ago by
Brussels
guillaume.dachy0 wrote:

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

locale:
[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. 

G. 

ADD COMMENTlink written 20 months ago by guillaume.dachy0
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