Files in markgene/yamatClassifier

Yet Another Methylation Array Toolkit: Classifier

R/batch-effect-correction.R R/batch-effect-explore-beta.R R/batch-effect-explore-meth.R R/batch-effect-explore-unmeth.R R/batch-effect-explore.R R/corrplot.R R/feature-selection.R R/most-variable.R R/pca-plot.R R/pca.R R/preprocess_dkfz.R R/probe.R R/relative-log-expression.R R/tmp.R R/tmp2.R R/train_model1.R R/train_model2.R R/train_model3.R R/train_model4.R R/train_model5.R R/train_preprocess_pipe.R R/trainer.R R/tsne.R R/utils.R README.md man/compute_relative_log_expression.Rd man/cor_mtest.Rd man/correlogram.Rd man/create_trainer.Rd man/cross_validate_model5.Rd man/density_plot_row_sd.Rd man/diagnose_tsne.coord.Rd man/diagnose_tsne.cor.Rd man/explore_batch_effect.Rd man/explore_batch_effect_beta_value.Rd man/explore_batch_effect_beta_value_pca_compute.Rd man/explore_batch_effect_beta_value_rle.Rd man/explore_batch_effect_meth.Rd man/explore_batch_effect_meth_pca_compute.Rd man/explore_batch_effect_meth_rle.Rd man/explore_batch_effect_unmeth.Rd man/explore_batch_effect_unmeth_pca_compute.Rd man/explore_batch_effect_unmeth_rle.Rd man/find_pc_number.capper.Rd man/find_pc_number.var_frac.Rd man/find_pc_number.yamat.Rd man/get_and_filter_probes.Rd man/get_batch_effect_explore_dir.Rd man/get_batch_matrix.Rd man/get_beta_value.Rd man/get_beta_value_adjusted.Rd man/get_beta_value_adjusted_rda.Rd man/get_main_pca_plot.Rd man/get_meth.Rd man/get_meth_from_preprocessed_files.Rd man/get_preprocessed_dir.Rd man/get_probes.Rd man/get_probes_from_scratch.Rd man/get_probes_rda.Rd man/get_targets.Rd man/get_trainer_rda.Rd man/get_unmeth.Rd man/get_unmeth_from_preprocessed_files.Rd man/get_x_density_plot.Rd man/get_y_density_plot.Rd man/most_variable.Rd man/multiplot_tsne.Rd man/pca.Rd man/pca123.Rd man/plot_pca_result.Rd man/plot_relative_log_expression.Rd man/plot_tsne.Rd man/prepare_plot_data.Rd man/preprocess_dkfz.Rd man/project_pc.Rd man/run_fitsne.Rd man/run_rtsne.Rd man/select_features_boruta.Rd man/select_features_boruta2.Rd man/select_features_ranger.Rd man/shuffle_matrix.Rd man/train_batch_effect_model.Rd man/train_calibration_model_ridge.Rd man/train_model1.Rd man/train_model1_inner_fold.Rd man/train_model1_outer_fold.Rd man/train_model2.Rd man/train_model2_inner_fold.Rd man/train_model2_outer_fold.Rd man/train_model3.Rd man/train_model3_inner_fold.Rd man/train_model3_outer_fold.Rd man/train_model4.Rd man/train_model4_inner_fold.Rd man/train_model4_outer_fold.Rd man/train_model5_inner_fold.Rd man/train_model5_outer_fold.Rd man/train_preprocess_pipe.Rd man/tsne.Rd tests/testthat.R tests/testthat/test_corrplot.R tests/testthat/test_create_trainer.R tests/testthat/test_cross_validate_model5.R tests/testthat/test_explore_batch_effect.R tests/testthat/test_feature_selection_boruta.R tests/testthat/test_feature_selection_boruta2.R tests/testthat/test_feature_selection_ranger.R tests/testthat/test_get_beta_value.R tests/testthat/test_get_meth.R tests/testthat/test_get_preprocessed_dir.R tests/testthat/test_get_probes.R tests/testthat/test_get_unmeth.R tests/testthat/test_pca.R tests/testthat/test_pca_plot.R tests/testthat/test_preprocess_dkfz.R tests/testthat/test_run_fitsne.R tests/testthat/test_run_rtsne.R tests/testthat/test_train_batch_effect_model.R tests/testthat/test_train_model1.R tests/testthat/test_train_model2.R tests/testthat/test_train_model3.R tests/testthat/test_train_model4.R tests/testthat/test_tsne.R vignettes/solid-tumor-example.Rmd