Entering edit mode
mwjnorris
▴
10
@user-24025
Last seen 4.3 years 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
