Loading required package: devtools Loading required package: usethis Error in get(genname, envir = envir) : object 'testthat_print' not found Loading required package: methylKit Loading required package: GenomicRanges Loading required package: stats4 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, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, 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, which, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Registered S3 method overwritten by 'R.oo': method from throw.default R.methodsS3 Loading required package: dplyr Attaching package: ‘dplyr’ The following object is masked from ‘package:methylKit’: select The following objects are masked from ‘package:GenomicRanges’: intersect, setdiff, union The following object is masked from ‘package:GenomeInfoDb’: intersect The following objects are masked from ‘package:IRanges’: collapse, desc, intersect, setdiff, slice, union The following objects are masked from ‘package:S4Vectors’: first, intersect, rename, setdiff, setequal, union The following objects are masked from ‘package:BiocGenerics’: combine, intersect, setdiff, union The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /gscratch/sw/intel-2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_rt.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] dplyr_0.8.3 methylKit_1.17.4 GenomicRanges_1.38.0 [4] GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.4 [7] BiocGenerics_0.32.0 devtools_2.1.0 usethis_1.5.1 loaded via a namespace (and not attached): [1] Biobase_2.46.0 pkgload_1.0.2 [3] splines_3.6.0 R.utils_2.9.0 [5] gtools_3.8.1 assertthat_0.2.1 [7] GenomeInfoDbData_1.2.2 Rsamtools_2.2.3 [9] remotes_2.1.0 sessioninfo_1.1.1 [11] numDeriv_2016.8-1.1 pillar_1.4.2 [13] backports_1.1.4 lattice_0.20-38 [15] glue_1.3.1 limma_3.42.2 [17] bbmle_1.0.23.1 digest_0.6.20 [19] XVector_0.26.0 qvalue_2.18.0 [21] colorspace_1.4-1 Matrix_1.2-17 [23] R.oo_1.22.0 plyr_1.8.4 [25] XML_3.98-1.20 pkgconfig_2.0.2 [27] emdbook_1.3.12 zlibbioc_1.32.0 [29] purrr_0.3.2 mvtnorm_1.0-11 [31] scales_1.0.0 processx_3.4.0 [33] BiocParallel_1.20.1 tibble_2.1.3 [35] ggplot2_3.2.0 withr_2.1.2 [37] SummarizedExperiment_1.16.1 lazyeval_0.2.2 [39] cli_1.1.0 magrittr_1.5 [41] crayon_1.3.4 mclust_5.4.5 [43] memoise_1.1.0 ps_1.3.0 [45] R.methodsS3_1.7.1 fs_1.3.1 [47] MASS_7.3-51.4 pkgbuild_1.0.3 [49] tools_3.6.0 data.table_1.12.2 [51] prettyunits_1.0.2 matrixStats_0.54.0 [53] stringr_1.4.0 munsell_0.5.0 [55] DelayedArray_0.12.3 callr_3.3.0 [57] Biostrings_2.54.0 compiler_3.6.0 [59] fastseg_1.32.0 rlang_0.4.10 [61] grid_3.6.0 RCurl_1.98-1.3 [63] bitops_1.0-7 testthat_2.1.1 [65] gtable_0.3.0 reshape2_1.4.3 [67] R6_2.4.0 GenomicAlignments_1.22.1 [69] rtracklayer_1.46.0 bdsmatrix_1.3-4 [71] rprojroot_1.3-2 desc_1.2.0 [73] stringi_1.4.3 Rcpp_1.0.1 [75] tidyselect_0.2.5 coda_0.19-3 sampleID slide.label pHTreatment 1 1 02-T1 1 2 2 04-T3 1 3 3 06-T1 1 4 4 08-T2 1 5 5 11-T4 0 6 6 UK-02 0 Received list of locations. Reading file. Reading file. Reading file. Reading file. Reading file. Reading file. Reading file. Reading file. nameBase nameBase2 1 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 2 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 3 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 4 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 5 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 6 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage sample.ID 1 1 2 2 3 3 4 4 5 5 6 6 nameBase nameBase2 1 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 2 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 3 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 4 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 5 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage 6 general-stats/percent-CpG-methylation general-stats/percent-CpG-coverage sample.ID 1 1 2 2 3 3 4 4 5 5 6 6 actualFileName1 1 general-stats/percent-CpG-methylation-Filtered-5xCoverage-Sample1.jpeg 2 general-stats/percent-CpG-methylation-Filtered-5xCoverage-Sample2.jpeg 3 general-stats/percent-CpG-methylation-Filtered-5xCoverage-Sample3.jpeg 4 general-stats/percent-CpG-methylation-Filtered-5xCoverage-Sample4.jpeg 5 general-stats/percent-CpG-methylation-Filtered-5xCoverage-Sample5.jpeg 6 general-stats/percent-CpG-methylation-Filtered-5xCoverage-Sample6.jpeg actualFileName2 1 general-stats/percent-CpG-coverage-Filtered-5xCoverage-Sample1.jpeg 2 general-stats/percent-CpG-coverage-Filtered-5xCoverage-Sample2.jpeg 3 general-stats/percent-CpG-coverage-Filtered-5xCoverage-Sample3.jpeg 4 general-stats/percent-CpG-coverage-Filtered-5xCoverage-Sample4.jpeg 5 general-stats/percent-CpG-coverage-Filtered-5xCoverage-Sample5.jpeg 6 general-stats/percent-CpG-coverage-Filtered-5xCoverage-Sample6.jpeg uniting... methylBase object with 6 rows -------------- chr start end strand coverage1 numCs1 numTs1 coverage2 numCs2 numTs2 1 NC_001276.1 123 125 * 1247 7 1240 948 6 942 2 NC_001276.1 305 307 * 1058 3 1055 728 2 726 3 NC_001276.1 433 435 * 1364 3 1361 1038 1 1037 4 NC_001276.1 457 459 * 1490 2 1488 1159 6 1153 5 NC_001276.1 482 484 * 1350 6 1344 1056 4 1052 6 NC_001276.1 609 611 * 1514 1 1513 1140 6 1134 coverage3 numCs3 numTs3 coverage4 numCs4 numTs4 coverage5 numCs5 numTs5 1 1011 2 1009 1393 7 1386 1106 5 1101 2 641 2 639 956 4 952 771 4 767 3 1063 2 1061 1403 4 1399 1130 5 1125 4 1157 2 1155 1543 3 1540 1274 1 1273 5 999 1 998 1367 4 1363 1161 5 1156 6 1162 3 1159 1499 5 1494 1366 9 1357 coverage6 numCs6 numTs6 coverage7 numCs7 numTs7 coverage8 numCs8 numTs8 1 1016 6 1010 1681 2 1679 874 4 870 2 763 7 756 1265 2 1263 598 0 598 3 1225 4 1221 1934 9 1925 973 5 968 4 1315 4 1311 2130 7 2123 1049 8 1041 5 1135 6 1129 1874 4 1870 921 6 915 6 1312 0 1312 2125 4 2121 1024 2 1022 -------------- sample.ids: 1 2 3 4 5 6 7 8 destranded FALSE assembly: Roslin context: CpG treament: 1 1 1 1 0 0 0 0 resolution: base The "ward" method has been renamed to "ward.D"; note new "ward.D2" 1 2 3 4 5 6 7 1 1.0000000 0.8866512 0.8915522 0.8930416 0.8893683 0.8908096 0.8908262 2 0.8866512 1.0000000 0.8885542 0.8878933 0.8862618 0.8869660 0.8864356 3 0.8915522 0.8885542 1.0000000 0.8955072 0.8911519 0.8927544 0.8925871 4 0.8930416 0.8878933 0.8955072 1.0000000 0.8907836 0.8936962 0.8969419 5 0.8893683 0.8862618 0.8911519 0.8907836 1.0000000 0.8911283 0.8896332 6 0.8908096 0.8869660 0.8927544 0.8936962 0.8911283 1.0000000 0.8906776 7 0.8908262 0.8864356 0.8925871 0.8969419 0.8896332 0.8906776 1.0000000 8 0.8869940 0.8870476 0.8902513 0.8894000 0.8886130 0.8891598 0.8859170 8 1 0.8869940 2 0.8870476 3 0.8902513 4 0.8894000 5 0.8886130 6 0.8891598 7 0.8859170 8 1.0000000 null device 1 The "ward" method has been renamed to "ward.D"; note new "ward.D2" Call: hclust(d = d, method = HCLUST.METHODS[hclust.method]) Cluster method : ward.D Distance : pearson Number of objects: 8 null device 1 null device 1 null device 1 The "ward" method has been renamed to "ward.D"; note new "ward.D2" Call: hclust(d = d, method = HCLUST.METHODS[hclust.method]) Cluster method : ward.D Distance : pearson Number of objects: 6 null device 1 null device 1 null device 1 stage 1 2 2 1 3 1 4 1 5 2 6 3 two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) There were 50 or more warnings (use warnings() to see the first 50) Error in head(differentialMethylationStatsTreatment) : object 'differentialMethylationStatsTreatment' not found Execution halted