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I try to use missMethyl to do gometh function for EPICv2 array, but it fails to do so. The latest released version should be formally support EPICv2. I have downloaded the latest version of missmethyl When I type ?gometh, it shows only array.type = c("450K", "EPIC"), no option for EPICv2. Despite the reference manual clear states we can select EPICv2 How can I solve the problem? Thanks.
sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Asia/Hong_Kong
tzcode source: internal
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] missMethyl_1.38.0 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
[4] minfi_1.50.0 bumphunter_1.46.0 locfit_1.5-9.10
[7] iterators_1.0.14 foreach_1.5.2 Biostrings_2.72.1
[10] XVector_0.44.0 SummarizedExperiment_1.34.0 Biobase_2.64.0
[13] MatrixGenerics_1.16.0 matrixStats_1.3.0 GenomicRanges_1.56.1
[16] GenomeInfoDb_1.40.1 IRanges_2.38.1 S4Vectors_0.42.1
[19] BiocGenerics_0.50.0 BiocManager_1.30.23
loaded via a namespace (and not attached):
[1] splines_4.4.1 BiocIO_1.14.0 bitops_1.0-8 filelock_1.0.3 tibble_3.2.1 R.oo_1.26.0
[7] preprocessCore_1.66.0 XML_3.99-0.17 rpart_4.1.23 lifecycle_1.0.4 httr2_1.0.2 edgeR_4.2.1
[13] base64_2.0.1 lattice_0.22-6 ensembldb_2.28.0 MASS_7.3-60.2 scrime_1.3.5 backports_1.5.0
[19] magrittr_2.0.3 limma_3.60.4 Hmisc_5.1-3 rmarkdown_2.27 yaml_2.3.10 doRNG_1.8.6
[25] askpass_1.2.0 Gviz_1.48.0 DBI_1.2.3 RColorBrewer_1.1-3 DMRcate_3.0.5 abind_1.4-5
[31] zlibbioc_1.50.0 quadprog_1.5-8 purrr_1.0.2 R.utils_2.12.3 AnnotationFilter_1.28.0 biovizBase_1.52.0
[37] RCurl_1.98-1.16 nnet_7.3-19 VariantAnnotation_1.50.0 rappdirs_0.3.3 GenomeInfoDbData_1.2.12 genefilter_1.86.0
[43] pheatmap_1.0.12 annotate_1.82.0 permute_0.9-7 DelayedMatrixStats_1.26.0 codetools_0.2-20 DelayedArray_0.30.1
[49] DNAcopy_1.78.0 xml2_1.3.6 tidyselect_1.2.1 UCSC.utils_1.0.0 beanplot_1.3.1 BiocFileCache_2.12.0
[55] base64enc_0.1-3 illuminaio_0.46.0 GenomicAlignments_1.40.0 jsonlite_1.8.8 multtest_2.60.0 Formula_1.2-5
[61] survival_3.6-4 tools_4.4.1 progress_1.2.3 Rcpp_1.0.13 glue_1.7.0 gridExtra_2.3
[67] SparseArray_1.4.8 xfun_0.46 dplyr_1.1.4 HDF5Array_1.32.0 fastmap_1.2.0 latticeExtra_0.6-30
[73] rhdf5filters_1.16.0 fansi_1.0.6 openssl_2.2.0 digest_0.6.36 R6_2.5.1 colorspace_2.1-1
[79] gtools_3.9.5 jpeg_0.1-10 dichromat_2.0-0.1 biomaRt_2.60.1 RSQLite_2.3.7 R.methodsS3_1.8.2
[85] tidyr_1.3.1 utf8_1.2.4 generics_0.1.3 data.table_1.15.4 rtracklayer_1.64.0 prettyunits_1.2.0
[91] httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.4.1 pkgconfig_2.0.3 gtable_0.3.5 blob_1.2.4
[97] siggenes_1.78.0 htmltools_0.5.8.1 ProtGenerics_1.36.0 scales_1.3.0 png_0.1-8 knitr_1.48
[103] rstudioapi_0.16.0 tzdb_0.4.0 rjson_0.2.21 nlme_3.1-164 checkmate_2.3.2 curl_5.2.1
[109] org.Hs.eg.db_3.19.1 cachem_1.1.0 rhdf5_2.48.0 stringr_1.5.1 BiocVersion_3.19.1 foreign_0.8-86
[115] AnnotationDbi_1.66.0 restfulr_0.0.15 GEOquery_2.72.0 pillar_1.9.0 grid_4.4.1 reshape_0.8.9
[121] vctrs_0.6.5 dbplyr_2.5.0 xtable_1.8-4 cluster_2.1.6 htmlTable_2.4.3 evaluate_0.24.0
[127] bsseq_1.40.0 readr_2.1.5 GenomicFeatures_1.56.0 cli_3.6.3 compiler_4.4.1 Rsamtools_2.20.0
[133] rngtools_1.5.2 rlang_1.1.4 crayon_1.5.3 nor1mix_1.3-3 mclust_6.1.1 interp_1.1-6
[139] maftools_2.20.0 plyr_1.8.9 stringi_1.8.4 deldir_2.0-4 BiocParallel_1.38.0 munsell_0.5.1
[145] lazyeval_0.2.2 Matrix_1.7-0 ExperimentHub_2.12.0 BSgenome_1.72.0 hms_1.1.3 sparseMatrixStats_1.16.0
[151] bit64_4.0.5 ggplot2_3.5.1 Rhdf5lib_1.26.0 KEGGREST_1.44.1 statmod_1.5.0 AnnotationHub_3.12.0
[157] memoise_2.0.1 bit_4.0.5
By version 1.38.0, I mean version 1.38.0 of
MissMethyl
.