In the processing of EPICv2, it is suggested that DMRcate should be run to remove replicate probes. However in the latest version of DMRcate, there is no such function of rmPosReps.
DMRcate::rmPosReps(M, filter.strategy="sensitivity") is not working. --> Error: 'rmPosReps' is not an exported object from 'namespace:DMRcate'
Instead this step is directly incorporated into cpgannotate function of DMRcate. So how can I remove the duplicate probes now? Thanks.
sessionInfo() R version 4.4.2 (2024-10-31 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 [4] LC_NUMERIC=C 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] DMRcate_3.2.0 DMRcatedata_2.24.0
[3] ExperimentHub_2.14.0 AnnotationHub_3.14.0
[5] BiocFileCache_2.14.0 dbplyr_2.5.0
[7] IlluminaHumanMethylationEPICv2manifest_1.0.0 BiocManager_1.30.25
[9] missMethyl_1.40.0 IlluminaHumanMethylationEPICv2anno.20a1.hg38_1.0.0
[11] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
[13] minfi_1.52.1 bumphunter_1.48.0
[15] locfit_1.5-9.10 iterators_1.0.14
[17] foreach_1.5.2 Biostrings_2.74.1
[19] XVector_0.46.0 SummarizedExperiment_1.36.0
[21] Biobase_2.66.0 MatrixGenerics_1.18.0
[23] matrixStats_1.4.1 GenomicRanges_1.58.0
[25] GenomeInfoDb_1.42.1 IRanges_2.40.1
[27] S4Vectors_0.44.0 BiocGenerics_0.52.0
[29] limma_3.62.1
loaded via a namespace (and not attached):
[1] splines_4.4.2 BiocIO_1.16.0 bitops_1.0-9 filelock_1.0.3
[5] BiasedUrn_2.0.12 cellranger_1.1.0 R.oo_1.27.0 tibble_3.2.1
[9] preprocessCore_1.68.0 XML_3.99-0.18 rpart_4.1.23 lifecycle_1.0.4
[13] httr2_1.0.7 edgeR_4.4.1 ensembldb_2.30.0 lattice_0.22-6
[17] MASS_7.3-61 base64_2.0.2 scrime_1.3.5 backports_1.5.0
[21] magrittr_2.0.3 rmarkdown_2.29 Hmisc_5.2-1 yaml_2.3.10
[25] doRNG_1.8.6 askpass_1.2.1 Gviz_1.50.0 DBI_1.2.3
[29] RColorBrewer_1.1-3 abind_1.4-8 zlibbioc_1.52.0 quadprog_1.5-8
[33] R.utils_2.12.3 purrr_1.0.2 AnnotationFilter_1.30.0 biovizBase_1.54.0
[37] RCurl_1.98-1.16 nnet_7.3-19 VariantAnnotation_1.52.0 rappdirs_0.3.3
[41] GenomeInfoDbData_1.2.13 rentrez_1.2.3 genefilter_1.88.0 annotate_1.84.0
[45] permute_0.9-7 DelayedMatrixStats_1.28.0 codetools_0.2-20 DelayedArray_0.32.0
[49] xml2_1.3.6 tidyselect_1.2.1 UCSC.utils_1.2.0 beanplot_1.3.1
[53] base64enc_0.1-3 illuminaio_0.48.0 GenomicAlignments_1.42.0 jsonlite_1.8.9
[57] multtest_2.62.0 Formula_1.2-5 survival_3.7-0 tools_4.4.2
[61] progress_1.2.3 Rcpp_1.0.13-1 glue_1.8.0 gridExtra_2.3
[65] SparseArray_1.6.0 xfun_0.49 dplyr_1.1.4 HDF5Array_1.34.0
[69] withr_3.0.2 fastmap_1.2.0 latticeExtra_0.6-30 rhdf5filters_1.18.0
[73] openssl_2.3.0 digest_0.6.37 mime_0.12 R6_2.5.1
[77] colorspace_2.1-1 GO.db_3.20.0 gtools_3.9.5 jpeg_0.1-10
[81] dichromat_2.0-0.1 biomaRt_2.62.0 RSQLite_2.3.9 R.methodsS3_1.8.2
[85] tidyr_1.3.1 generics_0.1.3 data.table_1.16.4 rtracklayer_1.66.0
[89] prettyunits_1.2.0 httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.6.0
[93] pkgconfig_2.0.3 gtable_0.3.6 blob_1.2.4 siggenes_1.80.0
[97] htmltools_0.5.8.1 ProtGenerics_1.38.0 scales_1.3.0 png_0.1-8
[101] knitr_1.49 rstudioapi_0.17.1 tzdb_0.4.0 rjson_0.2.23
[105] checkmate_2.3.2 nlme_3.1-166 curl_6.0.1 org.Hs.eg.db_3.20.0
[109] cachem_1.1.0 rhdf5_2.50.1 stringr_1.5.1 BiocVersion_3.20.0
[113] foreign_0.8-87 AnnotationDbi_1.68.0 restfulr_0.0.15 GEOquery_2.74.0
[117] pillar_1.10.0 grid_4.4.2 reshape_0.8.9 vctrs_0.6.5
[121] xtable_1.8-4 cluster_2.1.6 htmlTable_2.4.3 bsseq_1.42.0
[125] evaluate_1.0.1 readr_2.1.5 GenomicFeatures_1.58.0 cli_3.6.3
[129] compiler_4.4.2 Rsamtools_2.22.0 rlang_1.1.4 crayon_1.5.3
[133] rngtools_1.5.2 nor1mix_1.3-3 interp_1.1-6 mclust_6.1.1
[137] plyr_1.8.9 stringi_1.8.4 deldir_2.0-4 BiocParallel_1.40.0
[141] munsell_0.5.1 lazyeval_0.2.2 Matrix_1.7-1 BSgenome_1.74.0
[145] hms_1.1.3 sparseMatrixStats_1.18.0 bit64_4.5.2 ggplot2_3.5.1
[149] Rhdf5lib_1.28.0 KEGGREST_1.46.0 statmod_1.5.0 memoise_2.0.1
[153] bit_4.5.0.1 readxl_1.4.3
```
