2017-12-27 12:31:20 0.8 STATUS STARTED RnBeads Pipeline 2017-12-27 12:31:20 0.8 INFO Analysis Title: Example 3 2017-12-27 12:31:20 0.8 INFO Initialized report index and saved to index.html 2017-12-27 12:31:20 0.8 STATUS STARTED Loading Data 2017-12-27 12:31:20 0.8 INFO Number of cores: 1 2017-12-27 12:31:21 0.9 INFO Loading data of type "idat.dir" 2017-12-27 12:31:21 0.9 STATUS STARTED Loading Data from IDAT Files 2017-12-27 12:31:21 0.9 INFO Added column barcode to the provided sample annotation table 2017-12-27 12:31:21 0.9 INFO Detected platform: HumanMethylation450 2017-12-27 12:31:43 1.2 STATUS COMPLETED Loading Data from IDAT Files 2017-12-27 12:32:46 1.6 STATUS Loaded data from data 2017-12-27 12:32:47 1.7 STATUS Predicted gender for the loaded samples 2017-12-27 12:32:48 1.7 STATUS Added data loading section to the report 2017-12-27 12:32:48 1.7 STATUS Loaded 12 samples and 485577 sites 2017-12-27 12:32:48 1.7 INFO Output object is of type RnBeadRawSet 2017-12-27 12:32:48 1.7 STATUS COMPLETED Loading Data 2017-12-27 12:33:14 1.7 INFO Initialized report index and saved to index.html 2017-12-27 12:33:14 1.7 STATUS STARTED Quality Control 2017-12-27 12:33:14 1.7 INFO Number of cores: 1 2017-12-27 12:33:14 1.7 STATUS STARTED Quality Control Section 2017-12-27 12:33:41 1.7 STATUS Added quality control box plots 2017-12-27 12:35:49 1.7 STATUS Added quality control bar plots 2017-12-27 12:35:52 1.7 STATUS Added negative control boxplots 2017-12-27 12:35:52 1.7 STATUS COMPLETED Quality Control Section 2017-12-27 12:35:52 1.7 STATUS STARTED Visualizing SNP Probe Data 2017-12-27 12:35:52 1.7 STATUS STARTED Mixups Visualization Section 2017-12-27 12:36:00 1.7 STATUS Added SNP Heatmap 2017-12-27 12:36:00 1.7 STATUS Calculated Manhattan distances between samples based on SNP probes 2017-12-27 12:36:01 1.7 STATUS Added SNP-based Distances 2017-12-27 12:36:01 1.7 STATUS COMPLETED Mixups Visualization Section 2017-12-27 12:36:01 1.7 STATUS COMPLETED Visualizing SNP Probe Data 2017-12-27 12:36:06 1.7 STATUS COMPLETED Quality Control 2017-12-27 12:36:06 1.7 INFO Initialized report index and saved to index.html 2017-12-27 12:36:06 1.7 STATUS STARTED Preprocessing 2017-12-27 12:36:06 1.7 INFO Number of cores: 1 2017-12-27 12:36:06 1.7 STATUS STARTED Filtering Procedures I 2017-12-27 12:36:07 1.7 STATUS STARTED Removal of SNP-enriched Sites 2017-12-27 12:36:07 1.7 STATUS Removed 10131 sites using SNP criterion "3" 2017-12-27 12:36:08 1.7 STATUS Saved removed sites to /DEEP_fhgfs/projects/RnBeads/analysis/examples/example_3/reports/preprocessing_data/removed_sites_snp.csv 2017-12-27 12:36:08 1.7 STATUS Added a corresponding section to the report 2017-12-27 12:36:08 1.7 STATUS COMPLETED Removal of SNP-enriched Sites 2017-12-27 12:36:09 1.7 INFO Working with a p-value threshold of 0.05 2017-12-27 12:36:09 1.7 STATUS STARTED Greedycut 2017-12-27 12:36:17 1.6 STATUS Calculated a total of 758 iterations 2017-12-27 12:36:17 1.6 INFO Optimal number of iterations is 758 2017-12-27 12:36:21 1.6 STATUS Created ROC plot 2017-12-27 12:36:24 1.6 STATUS Created line plots for matrix dimensions and other statistics 2017-12-27 12:36:24 1.6 STATUS Saved removed sites to /DEEP_fhgfs/projects/RnBeads/analysis/examples/example_3/reports/preprocessing_data/removed_sites_greedycut.csv 2017-12-27 12:36:24 1.6 STATUS COMPLETED Greedycut 2017-12-27 12:36:24 1.6 STATUS Retained 12 samples and 474689 sites 2017-12-27 12:36:24 1.6 STATUS COMPLETED Filtering Procedures I 2017-12-27 12:36:24 1.6 STATUS STARTED Summary of Filtering Procedures I 2017-12-27 12:36:24 1.6 STATUS Creating summary table of removed sites, samples and unreliable measurements... 2017-12-27 12:36:26 1.7 STATUS Saving table and figures... 2017-12-27 12:36:27 1.7 STATUS Added summary table of removed and retained items 2017-12-27 12:36:27 1.7 INFO Subsampling 485577 sites for plotting density distributions 2017-12-27 12:36:29 1.7 STATUS Constructed sequences of removed and retained methylation values 2017-12-27 12:36:35 1.7 STATUS Added comparison between removed and retained beta values 2017-12-27 12:36:35 1.7 STATUS COMPLETED Summary of Filtering Procedures I 2017-12-27 12:36:35 1.7 STATUS STARTED Manipulating the object 2017-12-27 12:37:29 1.6 STATUS Removed 10888 sites (probes) 2017-12-27 12:37:30 1.6 INFO Retained 474689 sites and 12 samples 2017-12-27 12:37:30 1.6 STATUS COMPLETED Manipulating the object 2017-12-27 12:37:30 1.6 STATUS STARTED Normalization Procedure 2017-12-27 12:37:57 2.1 STATUS Performed normalization with method wm.dasen 2017-12-27 12:38:48 2.0 STATUS Performed normalization with method "wm.dasen" 2017-12-27 12:38:59 2.3 STATUS Added comparison between non-normalized and normalized beta values 2017-12-27 12:39:00 2.3 STATUS Added histogram of observed beta shifts (magnitude of correction) 2017-12-27 12:39:02 2.3 STATUS Added 2D histogram of observed beta values and shifts 2017-12-27 12:39:04 2.1 STATUS Added normalization section 2017-12-27 12:39:04 2.1 STATUS COMPLETED Normalization Procedure 2017-12-27 12:39:04 2.1 STATUS STARTED Filtering Procedures II 2017-12-27 12:39:05 2.1 INFO Imputation was skipped, data set may still contain missing methylation values 2017-12-27 12:39:05 2.1 STATUS STARTED Probe Context Removal 2017-12-27 12:39:05 2.1 STATUS Removed 3140 probe(s) having not acceptable context 2017-12-27 12:39:05 2.1 STATUS Saved removed sites to /DEEP_fhgfs/projects/RnBeads/analysis/examples/example_3/reports/preprocessing_data/removed_sites_context.csv 2017-12-27 12:39:05 2.1 STATUS Added a corresponding section to the report 2017-12-27 12:39:05 2.1 STATUS COMPLETED Probe Context Removal 2017-12-27 12:39:05 2.1 STATUS Retained 12 samples and 471549 sites 2017-12-27 12:39:05 2.1 STATUS COMPLETED Filtering Procedures II 2017-12-27 12:39:05 2.1 STATUS STARTED Summary of Filtering Procedures II 2017-12-27 12:39:05 2.1 STATUS Creating summary table of removed sites, samples and unreliable measurements... 2017-12-27 12:39:06 2.4 STATUS Saving table and figures... 2017-12-27 12:39:07 2.4 STATUS Added summary table of removed and retained items 2017-12-27 12:39:07 2.4 INFO Subsampling 474689 sites for plotting density distributions 2017-12-27 12:39:07 2.3 STATUS Constructed sequences of removed and retained methylation values 2017-12-27 12:39:13 2.3 STATUS Added comparison between removed and retained beta values 2017-12-27 12:39:13 2.3 STATUS COMPLETED Summary of Filtering Procedures II 2017-12-27 12:39:13 2.3 STATUS STARTED Manipulating the object 2017-12-27 12:40:05 1.9 STATUS Removed 3140 sites (probes) 2017-12-27 12:40:05 1.9 INFO Retained 471549 sites and 12 samples 2017-12-27 12:40:05 1.9 STATUS COMPLETED Manipulating the object 2017-12-27 12:40:05 1.9 STATUS COMPLETED Preprocessing 2017-12-27 12:40:26 1.9 INFO Initialized report index and saved to index.html 2017-12-27 12:40:26 1.9 STATUS STARTED Tracks and Tables 2017-12-27 12:40:26 1.9 INFO Number of cores: 1 2017-12-27 12:40:26 1.9 STATUS STARTED Generating Tracks and Tables 2017-12-27 12:40:26 1.9 STATUS STARTED Exporting sites 2017-12-27 12:40:26 1.9 STATUS STARTED Creating BED Files 2017-12-27 12:40:26 1.9 STATUS Converting to GRangesList 2017-12-27 12:40:31 2.0 STATUS Exporting sample 1 2017-12-27 12:40:33 2.0 STATUS Exporting sample 2 2017-12-27 12:40:36 2.0 STATUS Exporting sample 3 2017-12-27 12:40:38 2.0 STATUS Exporting sample 4 2017-12-27 12:40:40 2.0 STATUS Exporting sample 5 2017-12-27 12:40:43 2.0 STATUS Exporting sample 6 2017-12-27 12:40:45 2.0 STATUS Exporting sample 7 2017-12-27 12:40:47 2.0 STATUS Exporting sample 8 2017-12-27 12:40:50 2.0 STATUS Exporting sample 9 2017-12-27 12:40:52 2.0 STATUS Exporting sample 10 2017-12-27 12:40:56 2.0 STATUS Exporting sample 11 2017-12-27 12:40:58 2.0 STATUS Exporting sample 12 2017-12-27 12:41:00 2.0 STATUS COMPLETED Creating BED Files 2017-12-27 12:41:00 2.0 STATUS STARTED Creating Track Hub -- bigBed 2017-12-27 12:41:00 2.0 INFO Using /TL/deep-share/archive00/software/packages/R/R-devel_20171108_biocd/library/RnBeads/bin/linux_x86.64/bedToBigBed 2017-12-27 12:41:00 2.0 STATUS STARTED Conversion to BED 2017-12-27 12:41:22 2.0 STATUS COMPLETED Conversion to BED 2017-12-27 12:41:22 2.0 STATUS STARTED Creating Track Hub 2017-12-27 12:41:58 4.4 STATUS COMPLETED Creating Track Hub 2017-12-27 12:41:58 4.4 STATUS COMPLETED Creating Track Hub -- bigBed 2017-12-27 12:41:58 4.4 STATUS STARTED Creating UCSC Track Hub -- bigWig 2017-12-27 12:41:58 4.4 INFO Using /TL/deep-share/archive00/software/packages/R/R-devel_20171108_biocd/library/RnBeads/bin/linux_x86.64/bedGraphToBigWig 2017-12-27 12:41:58 4.4 STATUS STARTED Conversion to bedGraph 2017-12-27 12:42:16 4.5 STATUS COMPLETED Conversion to bedGraph 2017-12-27 12:42:16 4.5 STATUS STARTED Creating Track Hub 2017-12-27 12:42:33 4.5 STATUS COMPLETED Creating Track Hub 2017-12-27 12:42:33 4.5 STATUS COMPLETED Creating UCSC Track Hub -- bigWig 2017-12-27 12:42:33 4.5 STATUS COMPLETED Exporting sites 2017-12-27 12:42:33 4.5 STATUS COMPLETED Generating Tracks and Tables 2017-12-27 12:42:33 4.5 STATUS STARTED Writing export report 2017-12-27 12:42:45 4.4 STATUS COMPLETED Writing export report 2017-12-27 12:42:45 4.4 STATUS COMPLETED Tracks and Tables 2017-12-27 12:42:45 4.4 INFO Initialized report index and saved to index.html 2017-12-27 12:42:45 4.4 STATUS STARTED Covariate Inference 2017-12-27 12:42:45 4.4 INFO Number of cores: 1 2017-12-27 12:42:46 4.4 STATUS STARTED Age Prediction using predefined predictor 2017-12-27 12:42:47 4.5 STATUS COMPLETED Age Prediction using predefined predictor 2017-12-27 12:42:48 4.5 STATUS STARTED Adding Age Prediction Section to Report 2017-12-27 12:42:49 4.5 STATUS COMPLETED Adding Age Prediction Section to Report 2017-12-27 12:42:51 4.5 STATUS Calculated LUMP estimates 2017-12-27 12:42:51 4.5 STATUS STARTED Estimation of the cell type heterogeneity effects 2017-12-27 12:42:51 4.5 STATUS STARTED Performing computations 2017-12-27 13:02:41 4.4 STATUS COMPLETED Performing computations 2017-12-27 13:02:41 4.4 STATUS STARTED Adding a section to the report 2017-12-27 13:02:54 4.4 STATUS COMPLETED Adding a section to the report 2017-12-27 13:02:54 4.4 STATUS COMPLETED Estimation of the cell type heterogeneity effects 2017-12-27 13:02:54 4.4 INFO Added cell type covariates to the RnBSet object 2017-12-27 13:02:54 4.4 STATUS COMPLETED Covariate Inference 2017-12-27 13:03:15 4.4 INFO Initialized report index and saved to index.html 2017-12-27 13:03:15 4.4 STATUS STARTED Exploratory Analysis 2017-12-27 13:03:15 4.4 INFO Number of cores: 1 2017-12-27 13:03:16 4.4 STATUS Designed color mappings for probe type and CGI status 2017-12-27 13:03:35 4.8 STATUS STARTED Dimension Reduction Techniques 2017-12-27 13:03:35 5.2 STATUS STARTED MDS 2017-12-27 13:03:36 5.2 STATUS Calculated MDS coordinates using manhattan distance 2017-12-27 13:03:36 5.2 STATUS Calculated MDS coordinates using euclidean distance 2017-12-27 13:03:36 5.2 STATUS COMPLETED MDS 2017-12-27 13:03:36 5.2 STATUS STARTED PCA 2017-12-27 13:03:36 5.2 INFO Removed 15 loci ( sites ) because they contain missing values 2017-12-27 13:03:37 5.5 STATUS COMPLETED PCA 2017-12-27 13:03:37 5.6 STATUS STARTED MDS 2017-12-27 13:03:37 5.6 STATUS Calculated MDS coordinates using manhattan distance 2017-12-27 13:03:38 5.6 STATUS Calculated MDS coordinates using euclidean distance 2017-12-27 13:03:38 5.6 STATUS COMPLETED MDS 2017-12-27 13:03:38 5.6 STATUS STARTED PCA 2017-12-27 13:03:38 5.7 STATUS COMPLETED PCA 2017-12-27 13:03:38 5.7 STATUS STARTED MDS 2017-12-27 13:03:38 5.7 STATUS Calculated MDS coordinates using manhattan distance 2017-12-27 13:03:38 5.7 STATUS Calculated MDS coordinates using euclidean distance 2017-12-27 13:03:38 5.7 STATUS COMPLETED MDS 2017-12-27 13:03:38 5.7 STATUS STARTED PCA 2017-12-27 13:03:38 5.7 STATUS COMPLETED PCA 2017-12-27 13:03:38 5.7 STATUS STARTED MDS 2017-12-27 13:03:38 5.7 STATUS Calculated MDS coordinates using manhattan distance 2017-12-27 13:03:38 5.7 STATUS Calculated MDS coordinates using euclidean distance 2017-12-27 13:03:38 5.7 STATUS COMPLETED MDS 2017-12-27 13:03:38 5.7 STATUS STARTED PCA 2017-12-27 13:03:38 5.8 STATUS COMPLETED PCA 2017-12-27 13:03:38 5.8 STATUS STARTED MDS 2017-12-27 13:03:38 5.8 STATUS Calculated MDS coordinates using manhattan distance 2017-12-27 13:03:38 5.8 STATUS Calculated MDS coordinates using euclidean distance 2017-12-27 13:03:38 5.8 STATUS COMPLETED MDS 2017-12-27 13:03:38 5.8 STATUS STARTED PCA 2017-12-27 13:03:38 5.2 STATUS COMPLETED PCA 2017-12-27 13:03:38 5.2 INFO Mapping 4 traits to point colors and types 2017-12-27 13:15:16 4.7 INFO Principal components that explain at least 95 % of the total variance: 9 2017-12-27 13:15:16 4.7 INFO Saved percentage of total variance to pca_variance_explained_1.csv 2017-12-27 13:15:17 4.7 INFO Principal components that explain at least 95 % of the total variance: 9 2017-12-27 13:15:17 4.7 INFO Saved percentage of total variance to pca_variance_explained_2.csv 2017-12-27 13:15:18 4.7 INFO Principal components that explain at least 95 % of the total variance: 8 2017-12-27 13:15:18 4.7 INFO Saved percentage of total variance to pca_variance_explained_3.csv 2017-12-27 13:15:20 4.7 INFO Principal components that explain at least 95 % of the total variance: 8 2017-12-27 13:15:20 4.7 INFO Saved percentage of total variance to pca_variance_explained_4.csv 2017-12-27 13:15:21 4.7 INFO Principal components that explain at least 95 % of the total variance: 8 2017-12-27 13:15:21 4.7 INFO Saved percentage of total variance to pca_variance_explained_5.csv 2017-12-27 13:15:22 4.7 STATUS Created scatter plots and CDFs summarizing the reduced dimensional representations 2017-12-27 13:15:22 4.7 STATUS COMPLETED Dimension Reduction Techniques 2017-12-27 13:15:22 4.7 STATUS STARTED Tests for Associations 2017-12-27 13:15:22 4.7 INFO Testing the following traits for associations: Sample_Group; Cell_Line; Passage_No; Treatment; CellType; Predicted Male Probability; Predicted Gender; predicted_ages; Immune Cell Content (LUMP) 2017-12-27 13:15:22 4.7 STATUS Created 10000 sample permutations 2017-12-27 13:17:39 4.7 STATUS Computed correlations between principal components and traits. 2017-12-27 13:17:44 4.7 STATUS Computed pairwise correlations between traits. 2017-12-27 13:17:44 4.7 STATUS COMPLETED Tests for Associations 2017-12-27 13:17:59 4.7 STATUS STARTED Quality-associated Batch Effects 2017-12-27 13:20:40 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for sites 2017-12-27 13:21:33 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for sites 2017-12-27 13:22:27 4.7 STATUS Computed associations between 8 principal component(s) and extension for sites 2017-12-27 13:23:08 4.7 STATUS Computed associations between 8 principal component(s) and hybridization for sites 2017-12-27 13:24:02 4.7 STATUS Computed associations between 8 principal component(s) and non-polymorphic for sites 2017-12-27 13:26:40 4.7 STATUS Computed associations between 8 principal component(s) and specificity I for sites 2017-12-27 13:27:22 4.7 STATUS Computed associations between 8 principal component(s) and specificity II for sites 2017-12-27 13:29:07 4.7 STATUS Computed associations between 8 principal component(s) and staining for sites 2017-12-27 13:29:33 4.7 STATUS Computed associations between 8 principal component(s) and target removal for sites 2017-12-27 13:32:13 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for tiling 2017-12-27 13:33:07 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for tiling 2017-12-27 13:34:00 4.7 STATUS Computed associations between 8 principal component(s) and extension for tiling 2017-12-27 13:34:42 4.7 STATUS Computed associations between 8 principal component(s) and hybridization for tiling 2017-12-27 13:35:35 4.7 STATUS Computed associations between 8 principal component(s) and non-polymorphic for tiling 2017-12-27 13:38:15 4.7 STATUS Computed associations between 8 principal component(s) and specificity I for tiling 2017-12-27 13:38:55 4.7 STATUS Computed associations between 8 principal component(s) and specificity II for tiling 2017-12-27 13:40:41 4.7 STATUS Computed associations between 8 principal component(s) and staining for tiling 2017-12-27 13:41:08 4.7 STATUS Computed associations between 8 principal component(s) and target removal for tiling 2017-12-27 13:43:48 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for genes 2017-12-27 13:44:41 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for genes 2017-12-27 13:45:36 4.7 STATUS Computed associations between 8 principal component(s) and extension for genes 2017-12-27 13:46:16 4.7 STATUS Computed associations between 8 principal component(s) and hybridization for genes 2017-12-27 13:47:09 4.7 STATUS Computed associations between 8 principal component(s) and non-polymorphic for genes 2017-12-27 13:49:49 4.7 STATUS Computed associations between 8 principal component(s) and specificity I for genes 2017-12-27 13:50:29 4.7 STATUS Computed associations between 8 principal component(s) and specificity II for genes 2017-12-27 13:52:09 4.7 STATUS Computed associations between 8 principal component(s) and staining for genes 2017-12-27 13:52:37 4.7 STATUS Computed associations between 8 principal component(s) and target removal for genes 2017-12-27 13:55:16 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for promoters 2017-12-27 13:56:10 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for promoters 2017-12-27 13:57:05 4.7 STATUS Computed associations between 8 principal component(s) and extension for promoters 2017-12-27 13:57:45 4.7 STATUS Computed associations between 8 principal component(s) and hybridization for promoters 2017-12-27 13:58:38 4.7 STATUS Computed associations between 8 principal component(s) and non-polymorphic for promoters 2017-12-27 14:01:18 4.7 STATUS Computed associations between 8 principal component(s) and specificity I for promoters 2017-12-27 14:01:58 4.7 STATUS Computed associations between 8 principal component(s) and specificity II for promoters 2017-12-27 14:03:36 4.7 STATUS Computed associations between 8 principal component(s) and staining for promoters 2017-12-27 14:04:03 4.7 STATUS Computed associations between 8 principal component(s) and target removal for promoters 2017-12-27 14:06:42 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for cpgislands 2017-12-27 14:07:37 4.7 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for cpgislands 2017-12-27 14:08:31 4.7 STATUS Computed associations between 8 principal component(s) and extension for cpgislands 2017-12-27 14:09:10 4.7 STATUS Computed associations between 8 principal component(s) and hybridization for cpgislands 2017-12-27 14:10:04 4.7 STATUS Computed associations between 8 principal component(s) and non-polymorphic for cpgislands 2017-12-27 14:12:44 4.7 STATUS Computed associations between 8 principal component(s) and specificity I for cpgislands 2017-12-27 14:13:24 4.7 STATUS Computed associations between 8 principal component(s) and specificity II for cpgislands 2017-12-27 14:15:03 4.7 STATUS Computed associations between 8 principal component(s) and staining for cpgislands 2017-12-27 14:15:30 4.7 STATUS Computed associations between 8 principal component(s) and target removal for cpgislands 2017-12-27 14:18:48 4.7 STATUS Added heatmaps of correlation between principal components and signal levels of Q probes 2017-12-27 14:18:48 4.7 STATUS COMPLETED Quality-associated Batch Effects 2017-12-27 14:18:50 4.8 STATUS STARTED Methylation Value Distributions - Sample Groups 2017-12-27 14:18:50 4.8 INFO processing beta_density_samples_1_1 2017-12-27 14:18:50 4.8 INFO Density estimation ( all samples--sites ): Groupwise retained observations after missing value removal: all:5658573/5658588 2017-12-27 14:18:51 4.8 INFO Density estimation ( all samples--sites ): Groupwise retained observations after subsampling: all:1000000/5658573 2017-12-27 14:18:53 5.9 INFO processing beta_density_samples_1_2 2017-12-27 14:18:53 5.9 INFO Density estimation ( all samples--tiling ): Groupwise retained observations after missing value removal: all:1607400/1607400 2017-12-27 14:18:54 5.9 INFO Density estimation ( all samples--tiling ): Groupwise retained observations after subsampling: all:1000000/1607400 2017-12-27 14:18:56 6.1 INFO processing beta_density_samples_1_3 2017-12-27 14:18:56 6.1 INFO Density estimation ( all samples--genes ): Groupwise retained observations after missing value removal: all:369408/369408 2017-12-27 14:18:57 6.1 INFO processing beta_density_samples_1_4 2017-12-27 14:18:57 6.1 INFO Density estimation ( all samples--promoters ): Groupwise retained observations after missing value removal: all:371628/371628 2017-12-27 14:18:59 6.1 INFO processing beta_density_samples_1_5 2017-12-27 14:18:59 6.1 INFO Density estimation ( all samples--cpgislands ): Groupwise retained observations after missing value removal: all:319320/319320 2017-12-27 14:19:00 6.1 INFO processing beta_density_samples_2_1 2017-12-27 14:19:00 6.1 INFO Density estimation ( Sample_Group--sites ): Groupwise retained observations after missing value removal: hESC:2357739/2357745; hiPSC:3300834/3300843 2017-12-27 14:19:00 6.1 INFO Density estimation ( Sample_Group--sites ): Groupwise retained observations after subsampling: hESC:833333/2357739; hiPSC:1166667/3300834 2017-12-27 14:19:05 6.1 INFO processing beta_density_samples_2_2 2017-12-27 14:19:05 6.1 INFO Density estimation ( Sample_Group--tiling ): Groupwise retained observations after missing value removal: hESC:669750/669750; hiPSC:937650/937650 2017-12-27 14:19:09 6.1 INFO processing beta_density_samples_2_3 2017-12-27 14:19:09 6.1 INFO Density estimation ( Sample_Group--genes ): Groupwise retained observations after missing value removal: hESC:153920/153920; hiPSC:215488/215488 2017-12-27 14:19:11 6.1 INFO processing beta_density_samples_2_4 2017-12-27 14:19:11 6.1 INFO Density estimation ( Sample_Group--promoters ): Groupwise retained observations after missing value removal: hESC:154845/154845; hiPSC:216783/216783 2017-12-27 14:19:12 6.1 INFO processing beta_density_samples_2_5 2017-12-27 14:19:12 6.1 INFO Density estimation ( Sample_Group--cpgislands ): Groupwise retained observations after missing value removal: hESC:133050/133050; hiPSC:186270/186270 2017-12-27 14:19:14 6.1 INFO processing beta_density_samples_3_1 2017-12-27 14:19:14 6.1 INFO Density estimation ( Treatment--sites ): Groupwise retained observations after missing value removal: KOSR:943095/943098; TeSR:943095/943098 2017-12-27 14:19:19 6.1 INFO processing beta_density_samples_3_2 2017-12-27 14:19:19 6.1 INFO Density estimation ( Treatment--tiling ): Groupwise retained observations after missing value removal: KOSR:267900/267900; TeSR:267900/267900 2017-12-27 14:19:20 6.1 INFO processing beta_density_samples_3_3 2017-12-27 14:19:20 6.1 INFO Density estimation ( Treatment--genes ): Groupwise retained observations after missing value removal: KOSR:61568/61568; TeSR:61568/61568 2017-12-27 14:19:22 6.1 INFO processing beta_density_samples_3_4 2017-12-27 14:19:22 6.1 INFO Density estimation ( Treatment--promoters ): Groupwise retained observations after missing value removal: KOSR:61938/61938; TeSR:61938/61938 2017-12-27 14:19:23 6.1 INFO processing beta_density_samples_3_5 2017-12-27 14:19:23 6.1 INFO Density estimation ( Treatment--cpgislands ): Groupwise retained observations after missing value removal: KOSR:53220/53220; TeSR:53220/53220 2017-12-27 14:19:24 6.1 INFO processing beta_density_samples_4_1 2017-12-27 14:19:24 6.1 INFO Density estimation ( CellType--sites ): Groupwise retained observations after missing value removal: CT1:943094/943098; CT2:943096/943098 2017-12-27 14:19:28 6.2 INFO processing beta_density_samples_4_2 2017-12-27 14:19:28 6.2 INFO Density estimation ( CellType--tiling ): Groupwise retained observations after missing value removal: CT1:267900/267900; CT2:267900/267900 2017-12-27 14:19:30 6.2 INFO processing beta_density_samples_4_3 2017-12-27 14:19:30 6.2 INFO Density estimation ( CellType--genes ): Groupwise retained observations after missing value removal: CT1:61568/61568; CT2:61568/61568 2017-12-27 14:19:31 6.2 INFO processing beta_density_samples_4_4 2017-12-27 14:19:31 6.2 INFO Density estimation ( CellType--promoters ): Groupwise retained observations after missing value removal: CT1:61938/61938; CT2:61938/61938 2017-12-27 14:19:32 6.2 INFO processing beta_density_samples_4_5 2017-12-27 14:19:32 6.2 INFO Density estimation ( CellType--cpgislands ): Groupwise retained observations after missing value removal: CT1:53220/53220; CT2:53220/53220 2017-12-27 14:19:33 6.2 INFO processing beta_density_samples_5_1 2017-12-27 14:19:33 6.2 INFO Density estimation ( Predicted Gender--sites ): Groupwise retained observations after missing value removal: female:2829287/2829294; male:2829286/2829294 2017-12-27 14:19:34 6.2 INFO Density estimation ( Predicted Gender--sites ): Groupwise retained observations after subsampling: female:1000000/2829287; male:1000000/2829286 2017-12-27 14:19:39 6.0 INFO processing beta_density_samples_5_2 2017-12-27 14:19:39 6.0 INFO Density estimation ( Predicted Gender--tiling ): Groupwise retained observations after missing value removal: female:803700/803700; male:803700/803700 2017-12-27 14:19:43 6.1 INFO processing beta_density_samples_5_3 2017-12-27 14:19:43 6.1 INFO Density estimation ( Predicted Gender--genes ): Groupwise retained observations after missing value removal: female:184704/184704; male:184704/184704 2017-12-27 14:19:44 6.1 INFO processing beta_density_samples_5_4 2017-12-27 14:19:44 6.1 INFO Density estimation ( Predicted Gender--promoters ): Groupwise retained observations after missing value removal: female:185814/185814; male:185814/185814 2017-12-27 14:19:46 5.9 INFO processing beta_density_samples_5_5 2017-12-27 14:19:46 5.9 INFO Density estimation ( Predicted Gender--cpgislands ): Groupwise retained observations after missing value removal: female:159660/159660; male:159660/159660 2017-12-27 14:19:47 5.9 STATUS COMPLETED Methylation Value Distributions - Sample Groups 2017-12-27 14:19:47 5.9 STATUS STARTED Methylation Value Distributions - Probe Categories 2017-12-27 14:19:48 5.9 INFO Density estimation ( CGI Relation--all samples ): Groupwise retained observations after missing value removal: Open Sea:2019439/2019444; Shelf:546864/546864; Shore:1316412/1316412; Island:1775858/1775868 2017-12-27 14:19:48 5.9 INFO Density estimation ( CGI Relation--all samples ): Groupwise retained observations after subsampling: Open Sea:1427525/2019439; Shelf:386574/546864; Shore:930561/1316412; Island:1255340/1775858 2017-12-27 14:19:58 6.4 INFO Density estimation ( Design--all samples ): Groupwise retained observations after missing value removal: I:1593645/1593660; II:4064928/4064928 2017-12-27 14:19:58 6.4 INFO Density estimation ( Design--all samples ): Groupwise retained observations after subsampling: I:563267/1593645; II:1436733/4064928 2017-12-27 14:20:03 6.1 INFO Density estimation ( CGI Relation--hESC (based on Sample_Group) ): Groupwise retained observations after missing value removal: Open Sea:841434/841435; Shelf:227860/227860; Shore:548505/548505; Island:739940/739945 2017-12-27 14:20:09 6.1 INFO Density estimation ( Design--hESC (based on Sample_Group) ): Groupwise retained observations after missing value removal: I:664019/664025; II:1693720/1693720 2017-12-27 14:20:09 6.1 INFO Density estimation ( Design--hESC (based on Sample_Group) ): Groupwise retained observations after subsampling: I:563268/664019; II:1436732/1693720 2017-12-27 14:20:14 6.1 INFO Density estimation ( CGI Relation--hiPSC (based on Sample_Group) ): Groupwise retained observations after missing value removal: Open Sea:1178005/1178009; Shelf:319004/319004; Shore:767907/767907; Island:1035918/1035923 2017-12-27 14:20:23 6.1 INFO Density estimation ( Design--hiPSC (based on Sample_Group) ): Groupwise retained observations after missing value removal: I:929626/929635; II:2371208/2371208 2017-12-27 14:20:23 6.1 INFO Density estimation ( Design--hiPSC (based on Sample_Group) ): Groupwise retained observations after subsampling: I:563267/929626; II:1436733/2371208 2017-12-27 14:20:28 6.1 INFO Density estimation ( CGI Relation--KOSR (based on Treatment) ): Groupwise retained observations after missing value removal: Open Sea:336571/336574; Shelf:91144/91144; Shore:219402/219402; Island:295978/295978 2017-12-27 14:20:31 6.1 INFO Density estimation ( Design--KOSR (based on Treatment) ): Groupwise retained observations after missing value removal: I:265607/265610; II:677488/677488 2017-12-27 14:20:34 6.1 INFO Density estimation ( CGI Relation--TeSR (based on Treatment) ): Groupwise retained observations after missing value removal: Open Sea:336574/336574; Shelf:91144/91144; Shore:219402/219402; Island:295975/295978 2017-12-27 14:20:37 6.1 INFO Density estimation ( Design--TeSR (based on Treatment) ): Groupwise retained observations after missing value removal: I:265607/265610; II:677488/677488 2017-12-27 14:20:40 6.1 INFO Density estimation ( CGI Relation--CT1 (based on CellType) ): Groupwise retained observations after missing value removal: Open Sea:336573/336574; Shelf:91144/91144; Shore:219402/219402; Island:295975/295978 2017-12-27 14:20:43 6.1 INFO Density estimation ( Design--CT1 (based on CellType) ): Groupwise retained observations after missing value removal: I:265606/265610; II:677488/677488 2017-12-27 14:20:46 6.1 INFO Density estimation ( CGI Relation--CT2 (based on CellType) ): Groupwise retained observations after missing value removal: Open Sea:336574/336574; Shelf:91144/91144; Shore:219402/219402; Island:295976/295978 2017-12-27 14:20:49 6.1 INFO Density estimation ( Design--CT2 (based on CellType) ): Groupwise retained observations after missing value removal: I:265608/265610; II:677488/677488 2017-12-27 14:20:51 6.1 INFO Density estimation ( CGI Relation--female (based on Predicted Gender) ): Groupwise retained observations after missing value removal: Open Sea:1009719/1009722; Shelf:273432/273432; Shore:658206/658206; Island:887930/887934 2017-12-27 14:20:58 6.2 INFO Density estimation ( Design--female (based on Predicted Gender) ): Groupwise retained observations after missing value removal: I:796823/796830; II:2032464/2032464 2017-12-27 14:20:58 6.2 INFO Density estimation ( Design--female (based on Predicted Gender) ): Groupwise retained observations after subsampling: I:563268/796823; II:1436732/2032464 2017-12-27 14:21:04 6.1 INFO Density estimation ( CGI Relation--male (based on Predicted Gender) ): Groupwise retained observations after missing value removal: Open Sea:1009720/1009722; Shelf:273432/273432; Shore:658206/658206; Island:887928/887934 2017-12-27 14:21:11 6.1 INFO Density estimation ( Design--male (based on Predicted Gender) ): Groupwise retained observations after missing value removal: I:796822/796830; II:2032464/2032464 2017-12-27 14:21:11 6.1 INFO Density estimation ( Design--male (based on Predicted Gender) ): Groupwise retained observations after subsampling: I:563267/796822; II:1436733/2032464 2017-12-27 14:21:16 6.1 STATUS COMPLETED Methylation Value Distributions - Probe Categories 2017-12-27 14:21:16 6.1 STATUS STARTED Scatter Plots of Mean Beta vs Variance 2017-12-27 14:21:16 6.1 INFO Sample subgroups are defined by: Sample_Group; Treatment; CellType; Predicted Gender 2017-12-27 14:41:22 6.1 WARNING Removed 3 loci with missing values in group KOSR (based on Treatment) 2017-12-27 14:48:07 6.1 WARNING Removed 3 loci with missing values in group TeSR (based on Treatment) 2017-12-27 14:54:47 6.0 WARNING Removed 4 loci with missing values in group CT1 (based on CellType) 2017-12-27 15:01:30 6.0 WARNING Removed 2 loci with missing values in group CT2 (based on CellType) 2017-12-27 15:21:45 6.1 STATUS Created 36 scatter plots of methylation variance on the site level 2017-12-27 15:37:36 6.1 STATUS Created 72 scatter plots of methylation variance on the region level 2017-12-27 15:37:36 6.1 STATUS COMPLETED Scatter Plots of Mean Beta vs Variance 2017-12-27 15:37:36 6.1 STATUS STARTED Deviation Plots 2017-12-27 15:50:12 6.0 STATUS Created 27 deviation plots on the site level 2017-12-27 15:52:58 6.0 STATUS Created 36 deviation plots on the region level 2017-12-27 15:53:00 6.0 STATUS Added summary table of variabilities 2017-12-27 15:53:00 6.0 STATUS COMPLETED Deviation Plots 2017-12-27 15:53:00 6.0 STATUS STARTED Sample Clustering 2017-12-27 15:53:00 6.0 STATUS STARTED Agglomerative Hierarchical Clustering 2017-12-27 15:53:01 6.0 STATUS Performed clustering on sites using correlation as a distance metric 2017-12-27 15:53:01 6.0 STATUS Performed clustering on sites using manhattan as a distance metric 2017-12-27 15:53:02 6.0 STATUS Performed clustering on sites using euclidean as a distance metric 2017-12-27 15:53:02 6.0 STATUS Performed clustering on tiling using correlation as a distance metric 2017-12-27 15:53:02 6.0 STATUS Performed clustering on tiling using manhattan as a distance metric 2017-12-27 15:53:02 6.0 STATUS Performed clustering on tiling using euclidean as a distance metric 2017-12-27 15:53:02 6.0 STATUS Performed clustering on genes using correlation as a distance metric 2017-12-27 15:53:02 6.0 STATUS Performed clustering on genes using manhattan as a distance metric 2017-12-27 15:53:03 6.0 STATUS Performed clustering on genes using euclidean as a distance metric 2017-12-27 15:53:03 6.0 STATUS Performed clustering on promoters using correlation as a distance metric 2017-12-27 15:53:03 6.0 STATUS Performed clustering on promoters using manhattan as a distance metric 2017-12-27 15:53:03 6.0 STATUS Performed clustering on promoters using euclidean as a distance metric 2017-12-27 15:53:03 6.0 STATUS Performed clustering on cpgislands using correlation as a distance metric 2017-12-27 15:53:03 6.0 STATUS Performed clustering on cpgislands using manhattan as a distance metric 2017-12-27 15:53:03 6.0 STATUS Performed clustering on cpgislands using euclidean as a distance metric 2017-12-27 15:53:03 6.0 STATUS COMPLETED Agglomerative Hierarchical Clustering 2017-12-27 15:53:03 6.0 STATUS STARTED Clustering Section 2017-12-27 15:53:03 6.0 STATUS STARTED Generating Heatmaps 2017-12-27 15:53:03 6.0 STATUS STARTED Region type: sites 2017-12-27 15:59:17 6.0 STATUS COMPLETED Region type: sites 2017-12-27 15:59:17 6.0 STATUS STARTED Region type: tiling 2017-12-27 16:05:40 6.0 STATUS COMPLETED Region type: tiling 2017-12-27 16:05:40 6.0 STATUS STARTED Region type: genes 2017-12-27 16:11:57 6.0 STATUS COMPLETED Region type: genes 2017-12-27 16:11:57 6.0 STATUS STARTED Region type: promoters 2017-12-27 16:18:06 6.0 STATUS COMPLETED Region type: promoters 2017-12-27 16:18:06 6.0 STATUS STARTED Region type: cpgislands 2017-12-27 16:24:15 6.0 STATUS COMPLETED Region type: cpgislands 2017-12-27 16:24:15 6.0 STATUS Created 720 heatmaps based on the clustering results 2017-12-27 16:24:15 6.0 STATUS COMPLETED Generating Heatmaps 2017-12-27 16:24:15 6.0 STATUS STARTED Adding Color Legends 2017-12-27 16:26:01 6.0 STATUS COMPLETED Adding Color Legends 2017-12-27 16:26:01 6.0 STATUS STARTED Estimating Optimal Numbers of Clusters 2017-12-27 16:26:22 6.0 STATUS Estimated number of clusters based on mean silhouette value 2017-12-27 16:26:22 6.0 STATUS COMPLETED Estimating Optimal Numbers of Clusters 2017-12-27 16:26:22 6.0 STATUS STARTED Overlapping Clusters with Sample Traits 2017-12-27 16:26:22 6.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_1.csv 2017-12-27 16:26:22 6.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_2.csv 2017-12-27 16:26:22 6.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_3.csv 2017-12-27 16:26:22 6.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_4.csv 2017-12-27 16:26:23 6.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_5.csv 2017-12-27 16:26:42 6.0 STATUS COMPLETED Overlapping Clusters with Sample Traits 2017-12-27 16:26:42 6.0 STATUS COMPLETED Clustering Section 2017-12-27 16:26:42 6.0 STATUS COMPLETED Sample Clustering 2017-12-27 16:26:42 6.0 STATUS STARTED Drawing regional methylation profiles 2017-12-27 16:26:42 6.0 STATUS STARTED Creating a Corresponding Section in the Report 2017-12-27 16:26:44 6.0 STATUS Plotting region profiles for region genes and column all samples ... 2017-12-27 16:29:30 15.6 STATUS Plotting region profiles for region genes and column Sample_Group ... 2017-12-27 16:31:59 14.1 STATUS Plotting region profiles for region genes and column Treatment ... 2017-12-27 16:32:43 13.3 STATUS Plotting region profiles for region genes and column CellType ... 2017-12-27 16:33:27 10.9 STATUS Plotting region profiles for region genes and column Predicted Gender ... 2017-12-27 16:35:54 13.6 STATUS Plotting region profiles for region promoters and column all samples ... 2017-12-27 16:36:44 13.3 STATUS Plotting region profiles for region promoters and column Sample_Group ... 2017-12-27 16:37:31 13.8 STATUS Plotting region profiles for region promoters and column Treatment ... 2017-12-27 16:37:47 12.9 STATUS Plotting region profiles for region promoters and column CellType ... 2017-12-27 16:38:03 11.6 STATUS Plotting region profiles for region promoters and column Predicted Gender ... 2017-12-27 16:38:50 11.7 STATUS Plotting region profiles for region cpgislands and column all samples ... 2017-12-27 16:39:26 12.0 STATUS Plotting region profiles for region cpgislands and column Sample_Group ... 2017-12-27 16:39:59 11.8 STATUS Plotting region profiles for region cpgislands and column Treatment ... 2017-12-27 16:40:10 11.8 STATUS Plotting region profiles for region cpgislands and column CellType ... 2017-12-27 16:40:22 11.5 STATUS Plotting region profiles for region cpgislands and column Predicted Gender ... 2017-12-27 16:40:55 12.5 STATUS COMPLETED Creating a Corresponding Section in the Report 2017-12-27 16:40:55 12.5 STATUS COMPLETED Drawing regional methylation profiles 2017-12-27 16:40:55 12.5 STATUS COMPLETED Exploratory Analysis 2017-12-27 16:40:55 12.5 INFO Initialized report index and saved to index.html 2017-12-27 16:40:55 12.5 STATUS STARTED Differential Methylation 2017-12-27 16:40:55 12.5 INFO Number of cores: 1 2017-12-27 16:40:55 12.5 STATUS STARTED Analysis 2017-12-27 16:40:55 12.5 INFO Using 0 permutation tests 2017-12-27 16:40:55 12.5 INFO Using columns: Sample_ID,Sentrix_ID,Sentrix_Position,Sample_Plate,Sample_Well,Sample_Group,Passage_No,Treatment,barcode,Predicted Male Probability,Predicted Gender 2017-12-27 16:40:55 12.5 INFO Using region types: tiling,genes,promoters,cpgislands 2017-12-27 16:40:55 12.5 STATUS STARTED Retrieving comparison info 2017-12-27 16:40:55 12.5 WARNING The following samples were excluded from comparison 'hESC vs. hiPSC (based on Sample_Group)' because they contain missing values in the adjustment table:1,3,2,4 2017-12-27 16:40:56 12.5 WARNING The following samples were excluded from comparison 'female vs. male (based on Predicted Gender)' because they contain missing values in the adjustment table:3,1,2,4 2017-12-27 16:40:56 12.5 STATUS COMPLETED Retrieving comparison info 2017-12-27 16:40:56 12.5 STATUS STARTED Computing differential methylation tables 2017-12-27 16:40:56 12.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2017-12-27 16:40:56 12.5 STATUS STARTED Computing Differential Methylation Table 2017-12-27 16:40:56 12.5 INFO Adjusting for covariates: ct_1,ct_2 2017-12-27 16:40:56 12.5 INFO Conducting differential analysis using limma 2017-12-27 16:42:07 11.5 STATUS COMPLETED Computing Differential Methylation Table 2017-12-27 16:42:07 11.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2017-12-27 16:44:39 11.5 STATUS Computed table for tiling 2017-12-27 16:45:21 11.5 STATUS Computed table for genes 2017-12-27 16:46:01 11.5 STATUS Computed table for promoters 2017-12-27 16:46:37 11.5 STATUS Computed table for cpgislands 2017-12-27 16:46:37 11.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2017-12-27 16:46:37 11.5 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2017-12-27 16:46:37 11.5 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2017-12-27 16:46:37 11.5 STATUS STARTED Computing Differential Methylation Table 2017-12-27 16:46:38 11.5 INFO Adjusting for covariates: ct_1,ct_2 2017-12-27 16:46:38 11.5 INFO Conducting differential analysis using limma 2017-12-27 16:47:29 11.5 WARNING Could not compute p-values using limma: No residual degrees of freedom in linear model fits 2017-12-27 16:47:29 11.5 STATUS COMPLETED Computing Differential Methylation Table 2017-12-27 16:47:30 11.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2017-12-27 16:49:26 11.5 INFO 133950 p-values are NA. They are treated as 1 in FDR adjustment 2017-12-27 16:49:26 11.5 STATUS Computed table for tiling 2017-12-27 16:49:54 11.5 INFO 30784 p-values are NA. They are treated as 1 in FDR adjustment 2017-12-27 16:49:54 11.5 STATUS Computed table for genes 2017-12-27 16:50:21 11.5 INFO 30969 p-values are NA. They are treated as 1 in FDR adjustment 2017-12-27 16:50:21 11.5 STATUS Computed table for promoters 2017-12-27 16:50:45 11.5 INFO 26610 p-values are NA. They are treated as 1 in FDR adjustment 2017-12-27 16:50:45 11.5 STATUS Computed table for cpgislands 2017-12-27 16:50:45 11.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2017-12-27 16:50:45 11.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2017-12-27 16:50:45 11.5 STATUS STARTED Comparing: female vs. male (based on Predicted Gender) 2017-12-27 16:50:45 11.5 STATUS STARTED Computing Differential Methylation Table 2017-12-27 16:50:45 11.5 INFO Adjusting for covariates: ct_1,ct_2 2017-12-27 16:50:45 11.5 INFO Conducting differential analysis using limma 2017-12-27 16:51:46 11.5 STATUS COMPLETED Computing Differential Methylation Table 2017-12-27 16:51:47 11.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2017-12-27 16:54:14 11.5 STATUS Computed table for tiling 2017-12-27 16:54:56 11.5 STATUS Computed table for genes 2017-12-27 16:55:36 11.5 STATUS Computed table for promoters 2017-12-27 16:56:12 11.5 STATUS Computed table for cpgislands 2017-12-27 16:56:12 11.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2017-12-27 16:56:12 11.5 STATUS COMPLETED Comparing: female vs. male (based on Predicted Gender) 2017-12-27 16:56:12 11.5 STATUS COMPLETED Computing differential methylation tables 2017-12-27 16:56:12 11.5 INFO Skipping enrichment analysis of differentially methylated regions 2017-12-27 16:56:12 11.5 STATUS COMPLETED Analysis 2017-12-27 16:56:12 11.5 STATUS STARTED Saving temp objects for debugging 2017-12-27 16:56:27 11.5 STATUS COMPLETED Saving temp objects for debugging 2017-12-27 16:56:27 11.5 STATUS STARTED Report Generation 2017-12-27 16:56:27 11.5 STATUS Added introductory section 2017-12-27 16:56:27 11.5 STATUS STARTED Adding Site Level Information 2017-12-27 16:56:27 11.5 STATUS STARTED Selection of rank cutoffs 2017-12-27 16:56:28 11.5 STATUS COMPLETED Selection of rank cutoffs 2017-12-27 16:56:28 11.5 STATUS STARTED Adding scatterplots 2017-12-27 17:10:48 11.8 STATUS COMPLETED Adding scatterplots 2017-12-27 17:10:48 11.8 STATUS STARTED Adding volcano plots 2017-12-27 17:15:18 11.8 STATUS COMPLETED Adding volcano plots 2017-12-27 17:15:18 11.8 STATUS STARTED Adding tables 2017-12-27 17:16:06 11.8 STATUS COMPLETED Adding tables 2017-12-27 17:16:06 11.8 STATUS COMPLETED Adding Site Level Information 2017-12-27 17:16:06 11.8 STATUS STARTED Adding Region Level Information 2017-12-27 17:16:06 11.8 STATUS STARTED Selection of rank cutoffs 2017-12-27 17:16:06 11.8 STATUS COMPLETED Selection of rank cutoffs 2017-12-27 17:16:06 11.8 STATUS STARTED Adding scatterplots 2017-12-27 17:22:29 12.4 STATUS COMPLETED Adding scatterplots 2017-12-27 17:22:29 12.4 STATUS STARTED Adding volcano plots 2017-12-27 17:25:21 11.5 STATUS COMPLETED Adding volcano plots 2017-12-27 17:25:21 11.5 STATUS STARTED Adding tables 2017-12-27 17:25:36 11.5 STATUS COMPLETED Adding tables 2017-12-27 17:25:36 11.5 STATUS COMPLETED Adding Region Level Information 2017-12-27 17:25:36 11.5 STATUS COMPLETED Report Generation 2017-12-27 17:25:36 11.5 STATUS COMPLETED Differential Methylation 2017-12-27 17:25:36 11.5 INFO Initialized report index and saved to index.html 2017-12-27 17:25:37 11.5 STATUS STARTED Saving RData 2017-12-27 17:25:51 11.5 STATUS COMPLETED Saving RData 2017-12-27 17:25:51 11.5 STATUS COMPLETED RnBeads Pipeline