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Type 'q()' to quit R. > library(minfi) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: lattice Loading required package: GenomicRanges Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: colMeans, colSums, expand.grid, rowMeans, rowSums Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: Biostrings Loading required package: XVector Loading required package: bumphunter Loading required package: foreach Loading required package: iterators Loading required package: locfit locfit 1.5-9.1 2013-03-22 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > ## Needs to be uncompressed > manifestFile <- "../../../data_files/manifest_epic_v10b2/MethylationEPIC_v-1-0_B2.csv" > stopifnot(file.exists(manifestFile)) > maniTmp <- minfi:::read.manifest.EPIC(manifestFile) > > ## Checking > manifest <- maniTmp$manifest > address.all <- c(manifest$AddressA, manifest$AddressB) > sum(address.all == "") [1] 724612 > sum(is.na(address.all)) [1] 0 > address.all <- address.all[address.all != ""] > length(address.all) [1] 1009178 > stopifnot(!anyDuplicated(address.all)) > library(illuminaio) > epic <- readIDAT("../../../data_files/Demo_Data_EPIC/200144450018/200144450018_R04C01_Grn.idat") > address.epic <- as.character(epic$MidBlock) > sum(!address.epic %in% address.all) ## Set of addresses in the IDAT file not part of the manifest [1] 43463 > sum(! address.all %in% address.epic) ## set of addresses not in IDAT file. [1] 0 > nrow(manifest) [1] 866895 > any(manifest$AddressA != "" & !manifest$AddressA %in% address.epic) [1] FALSE > any(manifest$AddressB != "" & !manifest$AddressB %in% address.epic) [1] FALSE > wh <- which(manifest$AddressB != "" & !manifest$AddressB %in% address.epic) > tmp <- manifest[wh,] > table(tmp$Infinium_Design_Type) < table of extent 0 > > table(tmp$Color_Channel) < table of extent 0 > > table(tmp$Methyl450_Loci) < table of extent 0 > > > ## Controls ok > all(maniTmp$controls[,1] %in% address.epic) [1] TRUE > > ## Manifest package > maniList <- maniTmp$manifestList > ## Manually removing 1031 CpGs with missing addresses > ## dropCpGs <- manifest$Name[manifest$AddressB != "" & !manifest$AddressB %in% address.epic] > ## table(substr(dropCpGs, 1,2)) > ## maniList$TypeI <- maniList$TypeI[! maniList$TypeI$Name %in% dropCpGs,] > > IlluminaHumanMethylationEPICmanifest <- IlluminaMethylationManifest(TypeI = maniList$TypeI, + TypeII = maniList$TypeII, + TypeControl = maniList$TypeControl, + TypeSnpI = maniList$TypeSnpI, + TypeSnpII = maniList$TypeSnpII, + annotation = "IlluminaHumanMethylationEPIC") > stopifnot(validObject(IlluminaHumanMethylationEPICmanifest)) > save(IlluminaHumanMethylationEPICmanifest, compress = "xz", + file = "../../data/IlluminaHumanMethylationEPICmanifest.rda") > sessionInfo() R Under development (unstable) (2016-03-09 r70299) Platform: x86_64-apple-darwin15.3.0 (64-bit) Running under: OS X 10.11.3 (El Capitan) 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] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] illuminaio_0.13.1 minfi_1.17.8 [3] bumphunter_1.11.3 locfit_1.5-9.1 [5] iterators_1.0.8 foreach_1.4.3 [7] Biostrings_2.39.12 XVector_0.11.7 [9] SummarizedExperiment_1.1.22 GenomicRanges_1.23.24 [11] GenomeInfoDb_1.7.6 IRanges_2.5.40 [13] S4Vectors_0.9.43 lattice_0.20-33 [15] Biobase_2.31.3 BiocGenerics_0.17.3 loaded via a namespace (and not attached): [1] genefilter_1.53.2 splines_3.3.0 beanplot_1.2 [4] rtracklayer_1.31.7 GenomicFeatures_1.23.25 chron_2.3-47 [7] XML_3.98-1.4 survival_2.38-3 DBI_0.3.1 [10] BiocParallel_1.5.20 RColorBrewer_1.1-2 registry_0.3 [13] rngtools_1.2.4 doRNG_1.6 matrixStats_0.50.1 [16] plyr_1.8.3 pkgmaker_0.22 stringr_1.0.0 [19] zlibbioc_1.17.1 codetools_0.2-14 biomaRt_2.27.2 [22] AnnotationDbi_1.33.7 preprocessCore_1.33.0 Rcpp_0.12.3 [25] xtable_1.8-2 limma_3.27.13 base64_1.1 [28] annotate_1.49.1 Rsamtools_1.23.5 digest_0.6.9 [31] stringi_1.0-1 nor1mix_1.2-1 grid_3.3.0 [34] quadprog_1.5-5 GEOquery_2.37.0 tools_3.3.0 [37] bitops_1.0-6 magrittr_1.5 siggenes_1.45.0 [40] RCurl_1.95-4.8 RSQLite_1.0.0 MASS_7.3-45 [43] data.table_1.9.6 reshape_0.8.5 mclust_5.1 [46] GenomicAlignments_1.7.20 multtest_2.27.0 nlme_3.1-125 > rm(list = ls()) > > proc.time() user system elapsed 326.975 6.777 342.344