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When I was calling DMP.GUI to use interactive visualization to see my differential methylated probe results, it came with an warning, which says "error in evaluating the argument 'x' in selecting a method for function 'sort' ", and I cannot see the results in the interactive view.
How can I solve this problem? Thanks a lot.
Code should be placed in three backticks as shown below
# include your problematic code here with any corresponding output
myDMP <- champ.DMP(beta = myCombat,
pheno = myLoad$pd$Sample_Group,
adjPVal = 0.05,
adjust.method = "BH",
arraytype = "450K")
DMP.GUI(DMP = as.data.frame(myDMP[[1]]),
beta = myCombat,
pheno = myLoad$pd$Sample_Group)
# please also include the results of running the following in an R session
Listening on http://127.0.0.1:5420
<< Generating dmrplot >>
Warning: Error in <Anonymous>: error in evaluating the argument 'x' in selecting a method for function 'sort':
108: <Anonymous>
107: stop
106: Cutoff_repalce
102: renderPlotly
101: func
98: shinyRenderWidget
97: func
84: renderFunc
83: output$geneenrich
2: runApp
1: DMP.GUI
sessionInfo( )
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[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] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.54.0 forcats_0.5.2 stringr_1.5.0
[4] dplyr_1.1.0 purrr_1.0.1 readr_2.1.3
[7] tidyr_1.3.0 tibble_3.1.8 ggplot2_3.4.1
[10] tidyverse_1.3.2 shiny_1.7.3 doParallel_1.0.17
[13] ChAMP_2.28.0 RPMM_1.25 cluster_2.1.4
[16] DT_0.26 IlluminaHumanMethylationEPICmanifest_0.3.0 Illumina450ProbeVariants.db_1.34.0
[19] DMRcate_2.12.0 ChAMPdata_2.30.0 minfi_1.44.0
[22] bumphunter_1.40.0 locfit_1.5-9.6 iterators_1.0.14
[25] foreach_1.5.2 Biostrings_2.66.0 XVector_0.38.0
[28] SummarizedExperiment_1.28.0 Biobase_2.58.0 MatrixGenerics_1.10.0
[31] matrixStats_0.63.0 GenomicRanges_1.50.1 GenomeInfoDb_1.34.4
[34] IRanges_2.32.0 S4Vectors_0.36.1 BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 rtracklayer_1.58.0
[3] R.methodsS3_1.8.2 wateRmelon_2.4.0
[5] ragg_1.2.4 bit64_4.0.5
[7] knitr_1.42 DelayedArray_0.24.0
[9] R.utils_2.12.2 data.table_1.14.8
[11] rpart_4.1.19 KEGGREST_1.38.0
[13] RCurl_1.98-1.9 GEOquery_2.66.0
[15] AnnotationFilter_1.22.0 generics_0.1.3
[17] GenomicFeatures_1.50.2 preprocessCore_1.60.2
[19] RSQLite_2.2.19 combinat_0.0-8
[21] bit_4.0.5 tzdb_0.3.0
[23] lubridate_1.9.0 xml2_1.3.3
[25] httpuv_1.6.9 assertthat_0.2.1
[27] IlluminaHumanMethylation450kmanifest_0.4.0 gargle_1.2.1
[29] viridis_0.6.2 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[31] isva_1.9 xfun_0.37
[33] jquerylib_0.1.4 hms_1.1.2
[35] evaluate_0.20 missMethyl_1.32.1
[37] DNAcopy_1.72.3 promises_1.2.0.1
[39] fansi_1.0.4 restfulr_0.0.15
[41] scrime_1.3.5 progress_1.2.2
[43] readxl_1.4.1 dendextend_1.17.1
[45] dbplyr_2.2.1 DBI_1.1.3
[47] htmlwidgets_1.6.1 reshape_0.8.9
[49] googledrive_2.0.0 ROC_1.74.0
[51] ellipsis_0.3.2 crosstalk_1.2.0
[53] backports_1.4.1 permute_0.9-7
[55] annotate_1.76.0 biomaRt_2.54.0
[57] deldir_1.0-6 sparseMatrixStats_1.10.0
[59] vctrs_0.5.2 ensembldb_2.22.0
[61] withr_2.5.0 cachem_1.0.6
[63] globaltest_5.52.1 Gviz_1.42.1
[65] BSgenome_1.66.3 checkmate_2.1.0
[67] GenomicAlignments_1.34.0 prettyunits_1.1.1
[69] mclust_6.0.0 ExperimentHub_2.6.0
[71] lazyeval_0.2.2 crayon_1.5.2
[73] genefilter_1.80.3 labeling_0.4.2
[75] edgeR_3.40.0 pkgconfig_2.0.3
[77] nlme_3.1-160 ProtGenerics_1.30.0
[79] nnet_7.3-18 rlang_1.0.6
[81] lifecycle_1.0.3 nleqslv_3.3.4
[83] filelock_1.0.2 affyio_1.68.0
[85] BiocFileCache_2.6.0 modelr_0.1.10
[87] AnnotationHub_3.6.0 dichromat_2.0-0.1
[89] cellranger_1.1.0 rngtools_1.5.2
[91] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 base64_2.0.1
[93] Matrix_1.5-3 Rhdf5lib_1.20.0
[95] reprex_2.0.2 base64enc_0.1-3
[97] googlesheets4_1.0.1 geneLenDataBase_1.34.0
[99] viridisLite_0.4.1 png_0.1-8
[101] rjson_0.2.21 bitops_1.0-7
[103] R.oo_1.25.0 KernSmooth_2.23-20
[105] rhdf5filters_1.10.0 blob_1.2.3
[107] DelayedMatrixStats_1.20.0 doRNG_1.8.6
[109] qvalue_2.30.0 nor1mix_1.3-0
[111] jpeg_0.1-10 scales_1.2.1
[113] memoise_2.0.1 magrittr_2.0.3
[115] plyr_1.8.8 zlibbioc_1.44.0
[117] compiler_4.2.2 BiocIO_1.8.0
[119] RColorBrewer_1.1-3 illuminaio_0.40.0
[121] clue_0.3-64 Rsamtools_2.14.0
[123] cli_3.6.0 DSS_2.46.0
[125] affy_1.76.0 JADE_2.0-3
[127] htmlTable_2.4.1 Formula_1.2-5
[129] MASS_7.3-58.1 mgcv_1.8-41
[131] tidyselect_1.2.0 stringi_1.7.12
[133] textshaping_0.3.6 yaml_2.3.7
[135] askpass_1.1 latticeExtra_0.6-30
[137] grid_4.2.2 sass_0.4.5
[139] VariantAnnotation_1.44.1 timechange_0.1.1
[141] tools_4.2.2 rstudioapi_0.14
[143] foreign_0.8-84 bsseq_1.34.0
[145] gridExtra_2.3 farver_2.1.1
[147] digest_0.6.31 BiocManager_1.30.19
[149] quadprog_1.5-8 Rcpp_1.0.10
[151] broom_1.0.1 siggenes_1.72.0
[153] BiocVersion_3.16.0 later_1.3.0
[155] org.Hs.eg.db_3.16.0 httr_1.4.4
[157] AnnotationDbi_1.60.0 biovizBase_1.46.0
[159] lumi_2.50.0 colorspace_2.1-0
[161] rvest_1.0.3 fs_1.6.1
[163] XML_3.99-0.13 splines_4.2.2
[165] statmod_1.5.0 kpmt_0.1.0
[167] multtest_2.54.0 shinythemes_1.2.0
[169] systemfonts_1.0.4 plotly_4.10.1
[171] xtable_1.8-4 jsonlite_1.8.4
[173] marray_1.76.0 R6_2.5.1
[175] Hmisc_5.0-1 pillar_1.8.1
[177] htmltools_0.5.4 mime_0.12
[179] glue_1.6.2 fastmap_1.1.0
[181] BiocParallel_1.32.4 interactiveDisplayBase_1.36.0
[183] beanplot_1.3.1 codetools_0.2-18
[185] utf8_1.2.3 bslib_0.4.2
[187] lattice_0.20-45 sva_3.46.0
[189] BiasedUrn_2.0.9 curl_5.0.0
[191] gtools_3.9.4 GO.db_3.16.0
[193] openssl_2.0.5 interp_1.1-4
[195] survival_3.4-0 rmarkdown_2.20
[197] methylumi_2.44.0 fastICA_1.2-3
[199] munsell_0.5.0 rhdf5_2.42.0
[201] GenomeInfoDbData_1.2.9 goseq_1.50.0
[203] impute_1.72.3 HDF5Array_1.26.0
[205] haven_2.5.1 reshape2_1.4.4
[207] gtable_0.3.1
