Question: Error in YAPSA::annotate_intermut_dist_cohort
gravatar for TRASA
5 weeks ago by
TRASA0 wrote:


I tried to use the annotateintermutdist_cohort command from the YAPSA package on my VRangesList. However, I got following error message.i

> vr_dist <- annotate_intermut_dist_cohort(vrl, in_mode="min", in_verbose = TRUE)
Error in `[[<-`(`*tmp*`, name, value = c(1e+10, 248956422, 18778245, 4036160,  : 
  1049 elements in value to replace 464 elements

I went through the source code, but I could not really figure out what this error means and how I could solve it. Maybe I did something wrong when I generated the VRanges List. I have a list of vcf files that I combined in one VRangesList:

for (i in 1:length(list_vcf))
  vr = c(vr, readVcfAsVRanges(list_vcf[i], ref_genome, ScanVcfParam(geno=NA)))

(geno=NA because I have a few variants with AD<0 that I excluded that way)

  names(vr) <- sample_names
   vrl <- VRangesList(vr)
  VRangesList of length 252

Has anyone experienced the same error message? (In case you can suggest a more elegent way how to genertae the VRangesList, feel free to help as well)

session info()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] SomaticSignatures_2.18.0          NMF_0.21.0                        cluster_2.0.9                     rngtools_1.3.1                   
 [5] pkgmaker_0.27                     registry_0.5-1                    VariantAnnotation_1.28.13         Rsamtools_1.34.1                 
 [9] SummarizedExperiment_1.12.0       DelayedArray_0.8.0                BiocParallel_1.16.6               matrixStats_0.54.0               
[13] BSgenome.Hsapiens.UCSC.hg38_1.4.1 BSgenome_1.50.0                   rtracklayer_1.42.2                YAPSA_1.8.0                      
[17] bigmemory_4.5.33                  Biobase_2.42.0                    ggplot2_3.1.1                     GenomicRanges_1.34.0             
[21] GenomeInfoDb_1.18.2               Biostrings_2.50.2                 XVector_0.22.0                    IRanges_2.16.0                   
[25] S4Vectors_0.20.1                  BiocGenerics_0.28.0              

loaded via a namespace (and not attached):
  [1] bigmemory.sri_0.1.3      colorspace_1.4-1         rjson_0.2.20             biovizBase_1.30.1        circlize_0.4.6          
  [6] htmlTable_1.13.1         GlobalOptions_0.1.0      base64enc_0.1-3          dichromat_2.0-0          proxy_0.4-23            
 [11] rstudioapi_0.10          bit64_0.9-7              AnnotationDbi_1.44.0     codetools_0.2-16         splines_3.5.1           
 [16] ggbio_1.30.0             doParallel_1.0.14        lsei_1.2-0               knitr_1.23               Formula_1.2-3           
 [21] gridBase_0.4-7           png_0.1-7                graph_1.60.0             BiocManager_1.30.4       compiler_3.5.1          
 [26] httr_1.4.0               backports_1.1.4          assertthat_0.2.1         Matrix_1.2-17            lazyeval_0.2.2          
 [31] acepack_1.4.1            htmltools_0.3.6          prettyunits_1.0.2        tools_3.5.1              gtable_0.3.0            
 [36] glue_1.3.1               GenomeInfoDbData_1.2.0   reshape2_1.4.3           dplyr_0.8.1              PMCMR_4.3               
 [41] Rcpp_1.0.1               iterators_1.0.10         xfun_0.7                 stringr_1.4.0            ensembldb_2.6.8         
 [46] XML_3.98-1.19            dendextend_1.12.0        zlibbioc_1.28.0          scales_1.0.0             pcaMethods_1.74.0       
 [51] hms_0.4.2                ProtGenerics_1.14.0      RBGL_1.58.2              AnnotationFilter_1.6.0   RColorBrewer_1.1-2      
 [56] ComplexHeatmap_1.20.0    yaml_2.2.0               curl_3.3                 memoise_1.1.0            gridExtra_2.3           
 [61] biomaRt_2.38.0           rpart_4.1-15             reshape_0.8.8            latticeExtra_0.6-28      stringi_1.4.3           
 [66] RSQLite_2.1.1            corrplot_0.84            foreach_1.4.4            checkmate_1.9.3          GenomicFeatures_1.34.8  
 [71] bibtex_0.4.2             shape_1.4.4              rlang_0.3.4              pkgconfig_2.0.2          bitops_1.0-6            
 [76] lattice_0.20-38          purrr_0.3.2              GenomicAlignments_1.18.1 htmlwidgets_1.3          bit_1.1-14              
 [81] tidyselect_0.2.5         GGally_1.4.0             plyr_1.8.4               magrittr_1.5             R6_2.4.0                
 [86] Hmisc_4.2-0              DBI_1.0.0                pillar_1.4.1             foreign_0.8-71           withr_2.1.2             
 [91] survival_2.44-1.1        KEGGREST_1.22.0          RCurl_1.95-4.12          nnet_7.3-12              tibble_2.1.2            
 [96] crayon_1.3.4             OrganismDbi_1.24.0       viridis_0.5.1            GetoptLong_0.1.7         progress_1.2.2          
[101] data.table_1.12.2        blob_1.1.1               digest_0.6.19            xtable_1.8-4             munsell_0.5.0           
[106] viridisLite_0.3.0        gtrellis_1.14.0
yapsa • 41 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by TRASA0
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