Error in peak calling with Combp
1
Entering edit mode
mwjnorris • 10
@user-24025
Last seen 11 weeks ago

When running peak calling with combp with data from METAL based meta-analysis we get the following error...

Any help would be greatly appreciated.


> str(nat_vs_art_combp_filter)
'data.frame':   45151 obs. of  5 variables:
 $ V1: chr  "chr1" "chr1" "chr1" "chr1" ...
 $ V2: int  184943512 39957206 229694784 38273761 95700082 155532716 115053835 27114420 11865920 39457099 ...
 $ V3: int  184943512 39957206 229694784 38273761 95700082 155532716 115053835 27114420 11865920 39457099 ...
 $ V4: num  9.09e-22 3.69e-20 7.06e-20 1.95e-19 4.33e-19 ...
 $ V5: Factor w/ 455828 levels "cg00000029","cg00000108",..: 413831 287383 207196 397045 424258 339026 277278 303634 442510 414728 ...
> combp(nat_vs_art_combp_filter,dist.cutoff=1000,bin.size=310,seed=0.5,
+             region_plot=TRUE,mht_plot=TRUE,nCores=10)
Error in if (any(p.stouffer > 0.05)) { : 
  missing value where TRUE/FALSE needed



sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8     LC_MONETARY=en_AU.UTF-8   
 [6] LC_MESSAGES=en_AU.UTF-8    LC_PAPER=en_AU.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ENmix_1.22.6                                       doParallel_1.0.15                                  qqman_0.1.4                                       
 [4] RCircos_1.2.1                                      beeswarm_0.2.3                                     forestplot_1.10                                   
 [7] checkmate_2.0.0                                    magrittr_1.5                                       reshape2_1.4.4                                    
[10] gplots_3.0.4                                       eulerr_6.1.0                                       GEOquery_2.54.1                                   
[13] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 RColorBrewer_1.1-2                                 IlluminaHumanMethylation450kmanifest_0.4.0        
[16] topconfects_1.2.0                                  DMRcatedata_2.2.1                                  ExperimentHub_1.12.0                              
[19] AnnotationHub_2.18.0                               BiocFileCache_1.10.2                               dbplyr_1.4.4                                      
[22] DMRcate_2.0.7                                      limma_3.42.2                                       missMethyl_1.20.4                                 
[25] R.utils_2.9.2                                      R.oo_1.23.0                                        R.methodsS3_1.8.0                                 
[28] plyr_1.8.6                                         minfi_1.32.0                                       bumphunter_1.28.0                                 
[31] locfit_1.5-9.4                                     iterators_1.0.12                                   foreach_1.5.0                                     
[34] Biostrings_2.54.0                                  XVector_0.26.0                                     SummarizedExperiment_1.16.1                       
[37] DelayedArray_0.12.3                                BiocParallel_1.20.1                                matrixStats_0.56.0                                
[40] GenomicRanges_1.38.0                               GenomeInfoDb_1.22.1                                IRanges_2.20.2                                    
[43] Biobase_2.46.0                                     S4Vectors_0.24.4                                   BiocGenerics_0.32.0                               

loaded via a namespace (and not attached):
  [1] tidyselect_1.1.0                                    RSQLite_2.2.0                                       AnnotationDbi_1.48.0                               
  [4] htmlwidgets_1.5.1                                   lpSolve_5.6.15                                      munsell_0.5.0                                      
  [7] codetools_0.2-16                                    preprocessCore_1.48.0                               statmod_1.4.34                                     
 [10] colorspace_1.4-1                                    knitr_1.29                                          rstudioapi_0.11                                    
 [13] GenomeInfoDbData_1.2.2                              bit64_0.9-7.1                                       rhdf5_2.30.1                                       
 [16] vctrs_0.3.2                                         generics_0.0.2                                      xfun_0.16                                          
 [19] biovizBase_1.34.1                                   R6_2.4.1                                            illuminaio_0.28.0                                  
 [22] AnnotationFilter_1.10.0                             bitops_1.0-6                                        reshape_0.8.8                                      
 [25] assertthat_0.2.1                                    promises_1.1.1                                      scales_1.1.1                                       
 [28] bsseq_1.22.0                                        nnet_7.3-14                                         gtable_0.3.0                                       
 [31] methylumi_2.32.0                                    ensembldb_2.10.2                                    rlang_0.4.7                                        
 [34] genefilter_1.68.0                                   calibrate_1.7.7                                     splines_3.6.3                                      
 [37] rtracklayer_1.46.0                                  lazyeval_0.2.2                                      impute_1.60.0                                      
 [40] acepack_1.4.1                                       DSS_2.34.0                                          dichromat_2.0-0                                    
 [43] BiocManager_1.30.10                                 yaml_2.2.1                                          GenomicFeatures_1.38.2                             
 [46] backports_1.1.10                                    httpuv_1.5.4                                        Hmisc_4.4-0                                        
 [49] tools_3.6.3                                         nor1mix_1.3-0                                       ggplot2_3.3.2                                      
 [52] ellipsis_0.3.1                                      siggenes_1.60.0                                     dynamicTreeCut_1.63-1                              
 [55] Rcpp_1.0.5                                          base64enc_0.1-3                                     progress_1.2.2                                     
 [58] zlibbioc_1.32.0                                     purrr_0.3.4                                         RCurl_1.98-1.2                                     
 [61] BiasedUrn_1.07                                      prettyunits_1.1.1                                   rpart_4.1-15                                       
 [64] openssl_1.4.3                                       IlluminaHumanMethylationEPICmanifest_0.3.0          cluster_2.1.0                                      
 [67] data.table_1.13.0                                   packrat_0.5.0                                       ProtGenerics_1.18.0                                
 [70] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 RPMM_1.25                                           hms_0.5.3                                          
 [73] mime_0.9                                            xtable_1.8-4                                        XML_3.99-0.3                                       
 [76] jpeg_0.1-8.1                                        irr_0.84.1                                          readxl_1.3.1                                       
 [79] mclust_5.4.6                                        gridExtra_2.3                                       compiler_3.6.3                                     
 [82] biomaRt_2.42.1                                      tibble_3.0.3                                        KernSmooth_2.23-17                                 
 [85] crayon_1.3.4                                        htmltools_0.5.0                                     later_1.1.0.1                                      
 [88] Formula_1.2-3                                       geneplotter_1.64.0                                  tidyr_1.1.0                                        
 [91] DBI_1.1.0                                           MASS_7.3-53                                         rappdirs_0.3.1                                     
 [94] Matrix_1.2-18                                       readr_1.3.1                                         permute_0.9-5                                      
 [97] gdata_2.18.0                                        quadprog_1.5-8                                      Gviz_1.30.3                                        
[100] pkgconfig_2.0.3                                     GenomicAlignments_1.22.1                            foreign_0.8-76                                     
[103] xml2_1.3.2                                          annotate_1.64.0                                     rngtools_1.5                                       
[106] multtest_2.42.0                                     beanplot_1.2                                        ruv_0.9.7.1                                        
[109] doRNG_1.8.2                                         scrime_1.3.5                                        stringr_1.4.0                                      
[112] VariantAnnotation_1.32.0                            digest_0.6.25                                       cellranger_1.1.0                                   
[115] base64_2.0                                          htmlTable_2.0.1                                     edgeR_3.28.1                                       
[118] DelayedMatrixStats_1.8.0                            curl_4.3                                            shiny_1.5.0                                        
[121] Rsamtools_2.2.3                                     gtools_3.8.2                                        lifecycle_0.2.0                                    
[124] nlme_3.1-148                                        Rhdf5lib_1.8.0                                      askpass_1.1                                        
[127] BSgenome_1.54.0                                     pillar_1.4.6                                        lattice_0.20-41                                    
[130] fastmap_1.0.1                                       httr_1.4.2                                          survival_3.2-3                                     
[133] GO.db_3.10.0                                        interactiveDisplayBase_1.24.0                       glue_1.4.1                                         
[136] png_0.1-7                                           BiocVersion_3.10.1                                  bit_1.1-15.2                                       
[139] stringi_1.5.3                                       HDF5Array_1.14.4                                    blob_1.2.1                                         
[142] org.Hs.eg.db_3.10.0                                 caTools_1.18.0                                      latticeExtra_0.6-29                                
[145] memoise_1.1.0                                       dplyr_1.0.0
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