Hi, Does anyone know which is suitable R tools to perform analysis on illumina EPIC array? I tried to use minfi, but it seems I kept getting bugs for not being able to use function such as "read.metharray", or "read.metharray.exp".
> ?read.metharray No documentation for ‘read.metharray’ in specified packages and libraries: you could try ‘??read.metharray’ > sessionInfo() R version 3.2.5 (2016-04-14) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  minfi_1.14.0 bumphunter_1.8.0 locfit_1.5-9.1 iterators_1.0.8 foreach_1.4.3 Biostrings_2.36.4 XVector_0.8.0  GenomicRanges_1.20.8 GenomeInfoDb_1.4.3 IRanges_2.2.9 S4Vectors_0.6.6 lattice_0.20-33 Biobase_2.28.0 BiocGenerics_0.14.0  BiocInstaller_1.18.5 loaded via a namespace (and not attached):  genefilter_1.50.0 splines_3.2.5 beanplot_1.2 rtracklayer_1.28.10 GenomicFeatures_1.20.6 XML_3.98-1.4  survival_2.39-4 DBI_0.4-1 BiocParallel_1.2.22 RColorBrewer_1.1-2 registry_0.3 rngtools_1.2.4  lambda.r_1.1.7 doRNG_1.6 matrixStats_0.50.2 plyr_1.8.4 pkgmaker_0.22 stringr_1.0.0  zlibbioc_1.14.0 futile.logger_1.4.1 codetools_0.2-14 biomaRt_2.24.1 AnnotationDbi_1.30.1 illuminaio_0.10.0  preprocessCore_1.30.0 Rcpp_0.12.5 xtable_1.8-2 openssl_0.9.4 limma_3.24.15 base64_2.0  annotate_1.46.1 Rsamtools_1.20.5 digest_0.6.9 stringi_1.1.1 nor1mix_1.2-1 grid_3.2.5  GEOquery_2.34.0 quadprog_1.5-5 tools_3.2.5 bitops_1.0-6 magrittr_1.5 siggenes_1.42.0  RCurl_1.95-4.8 RSQLite_1.0.0 futile.options_1.0.0 MASS_7.3-45 Matrix_1.2-6 reshape_0.8.5  mclust_5.2 GenomicAlignments_1.4.2 multtest_2.24.0 nlme_3.1-128
Is its implementation completed? why did I get such errors? These commands are all listed in reference manual. By the way, is there other tools to analyze EPIC data? Thank you. -Xiaokuan