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Hi!
I'm performing methylation analysis using DMRcate to find the differentially methylated regions. I would now like to plot the fist DMR using DMR.plot(). However when I run it I get the following error: Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie. Any suggestions on how to solve this error?
DMR.plot(ranges=results.ranges1, dmr=1, CpGs=getBeta(GRSet.norm.na.good.noSnp.noXreact), what="Beta", arraytype = "EPIC", phen.col=cols, genome="hg19")
Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
sessionInfo( )
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.0
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Oslo
tzcode source: internal
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DMRcatedata_2.18.0 ExperimentHub_2.8.1
[3] AnnotationHub_3.8.0 BiocFileCache_2.8.0
[5] dbplyr_2.3.4 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[7] minfi_1.46.0 bumphunter_1.42.0
[9] locfit_1.5-9.8 iterators_1.0.14
[11] foreach_1.5.2 Biostrings_2.68.1
[13] XVector_0.40.0 SummarizedExperiment_1.30.2
[15] Biobase_2.60.0 MatrixGenerics_1.12.3
[17] matrixStats_1.0.0 GenomicRanges_1.52.1
[19] GenomeInfoDb_1.36.4 IRanges_2.34.1
[21] S4Vectors_0.38.2 BiocGenerics_0.46.0
[23] DMRcate_2.14.1 BiocManager_1.30.22
[25] ggplot2_3.4.4 corrplot_0.92
[27] rstatix_0.7.2 dplyr_1.1.3
loaded via a namespace (and not attached):
[1] splines_4.3.1 later_1.3.1
[3] BiocIO_1.10.0 bitops_1.0-7
[5] filelock_1.0.2 cellranger_1.1.0
[7] tibble_3.2.1 R.oo_1.25.0
[9] preprocessCore_1.62.1 XML_3.99-0.14
[11] rpart_4.1.21 lifecycle_1.0.3
[13] edgeR_3.42.4 base64_2.0.1
[15] MASS_7.3-60 lattice_0.21-9
[17] ensembldb_2.24.1 scrime_1.3.5
[19] backports_1.4.1 magrittr_2.0.3
[21] limma_3.56.2 Hmisc_5.1-1
[23] rmarkdown_2.25 yaml_2.3.7
[25] httpuv_1.6.12 doRNG_1.8.6
[27] askpass_1.2.0 Gviz_1.44.2
[29] DBI_1.1.3 RColorBrewer_1.1-3
[31] abind_1.4-5 zlibbioc_1.46.0
[33] quadprog_1.5-8 purrr_1.0.2
[35] R.utils_2.12.2 AnnotationFilter_1.24.0
[37] biovizBase_1.48.0 RCurl_1.98-1.12
[39] nnet_7.3-19 VariantAnnotation_1.46.0
[41] rappdirs_0.3.3 GenomeInfoDbData_1.2.10
[43] genefilter_1.82.1 annotate_1.78.0
[45] permute_0.9-7 DelayedMatrixStats_1.22.6
[47] codetools_0.2-19 DelayedArray_0.26.7
[49] xml2_1.3.5 tidyselect_1.2.0
[51] beanplot_1.3.1 base64enc_0.1-3
[53] illuminaio_0.42.0 GenomicAlignments_1.36.0
[55] multtest_2.56.0 ellipsis_0.3.2
[57] Formula_1.2-5 survival_3.5-7
[59] missMethyl_1.34.0 tools_4.3.1
[61] progress_1.2.2 Rcpp_1.0.11
[63] glue_1.6.2 gridExtra_2.3
[65] xfun_0.40 HDF5Array_1.28.1
[67] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 withr_2.5.1
[69] fastmap_1.1.1 latticeExtra_0.6-30
[71] rhdf5filters_1.12.1 fansi_1.0.5
[73] openssl_2.1.1 digest_0.6.33
[75] R6_2.5.1 mime_0.12
[77] colorspace_2.1-0 gtools_3.9.4
[79] jpeg_0.1-10 dichromat_2.0-0.1
[81] biomaRt_2.56.1 RSQLite_2.3.1
[83] R.methodsS3_1.8.2 utf8_1.2.4
[85] tidyr_1.3.0 generics_0.1.3
[87] data.table_1.14.8 rtracklayer_1.60.1
[89] prettyunits_1.2.0 httr_1.4.7
[91] htmlwidgets_1.6.2 S4Arrays_1.0.6
[93] pkgconfig_2.0.3 gtable_0.3.4
[95] blob_1.2.4 siggenes_1.74.0
[97] htmltools_0.5.6.1 carData_3.0-5
[99] ProtGenerics_1.32.0 scales_1.2.1
[101] png_0.1-8 knitr_1.44
[103] rstudioapi_0.15.0 tzdb_0.4.0
[105] rjson_0.2.21 nlme_3.1-163
[107] checkmate_2.2.0 curl_5.1.0
[109] org.Hs.eg.db_3.17.0 cachem_1.0.8
[111] rhdf5_2.44.0 stringr_1.5.0
[113] BiocVersion_3.17.1 foreign_0.8-85
[115] AnnotationDbi_1.62.2 restfulr_0.0.15
[117] GEOquery_2.68.0 reshape_0.8.9
[119] pillar_1.9.0 grid_4.3.1
[121] vctrs_0.6.4 promises_1.2.1
[123] car_3.1-2 xtable_1.8-4
[125] cluster_2.1.4 htmlTable_2.4.1
[127] evaluate_0.22 bsseq_1.36.0
[129] readr_2.1.4 GenomicFeatures_1.52.2
[131] cli_3.6.1 compiler_4.3.1
[133] Rsamtools_2.16.0 rngtools_1.5.2
[135] rlang_1.1.1 crayon_1.5.2
[137] nor1mix_1.3-0 mclust_6.0.0
[139] interp_1.1-4 plyr_1.8.9
[141] stringi_1.7.12 deldir_1.0-9
[143] BiocParallel_1.34.2 munsell_0.5.0
[145] lazyeval_0.2.2 DSS_2.48.0
[147] Matrix_1.6-1.1 BSgenome_1.68.0
[149] hms_1.1.3 sparseMatrixStats_1.12.2
[151] bit64_4.0.5 Rhdf5lib_1.22.1
[153] statmod_1.5.0 KEGGREST_1.40.1
[155] shiny_1.7.5.1 interactiveDisplayBase_1.38.0
[157] broom_1.0.5 memoise_2.0.1
[159] bit_4.0.5 readxl_1.4.3
