Files in markgene/yamat

Yet Another Methylation Array Toolkit

R/batch-effect.R R/beta-value-distribution-plots.R R/control-probes.R R/copy-number.R R/detection-pvalue.R R/gender.R R/geo.R R/get_qc_metrics.R R/normalize.R R/profile-repo.R R/qc-control-probes.R R/qc.R R/qc_pipe.R R/read.R R/report.R R/utils.R R/write_qc_metrics.R README.md man/control_probe_intensities.Rd man/copy_number.Rd man/create_idat_table.Rd man/dye_bias_correction.Rd man/get_bisulfite_converstion_type_1_green_qc.Rd man/get_bisulfite_converstion_type_1_red_qc.Rd man/get_bisulfite_converstion_type_2_qc.Rd man/get_control_probe_qc_metrics.Rd man/get_detection_p_value_qc_metrics.Rd man/get_extension_green_qc.Rd man/get_extension_red_qc.Rd man/get_gender.Rd man/get_gse.Rd man/get_hybridization_green_qc.Rd man/get_idat_file_list.Rd man/get_nonpolymorphic_green_qc.Rd man/get_nonpolymorphic_red_qc.Rd man/get_qc_metrics.Rd man/get_restoration_qc.Rd man/get_sentrix_id.Rd man/get_sentrix_position.Rd man/get_specificity_type_1_green_qc.Rd man/get_specificity_type_1_red_qc.Rd man/get_specificity_type_2_qc.Rd man/get_staining_green_qc.Rd man/get_staining_red_qc.Rd man/get_target_removal_qc.Rd man/ggsci_pal_d.Rd man/init_report.Rd man/is_annotated.Rd man/normalize.Rd man/normalize.dkfz.Rd man/normalize.methylcnv.Rd man/normalize.yamat.Rd man/plot_beta_value_histogram_fill_by_sample.Rd man/plot_control_probes.Rd man/qc.Rd man/qc_control_probes.Rd man/qc_pipe.Rd man/read_metharray_exp.Rd man/remove_batch_effect.Rd man/remove_batch_effect_beta.Rd man/remove_batch_effect_cn.Rd man/remove_batch_effect_mum.Rd man/set_annotation_epic_v2.Rd man/write_qc_metrics_excel.Rd tests/testthat.R tests/testthat/test_batch-effect.R tests/testthat/test_control-probes.R tests/testthat/test_control-probes_control_probe_intensities_450k.R tests/testthat/test_control-probes_control_probe_intensities_epic.R tests/testthat/test_copy-number.R tests/testthat/test_detection-pvalue_450k.R tests/testthat/test_geo.R tests/testthat/test_get_gender_450k.R tests/testthat/test_get_gender_epic.R tests/testthat/test_get_qc_metrics_epic.R tests/testthat/test_normalize.R tests/testthat/test_plot_beta_value_histogram_fill_by_sample_epic.R tests/testthat/test_qc-control-probes_epic.R tests/testthat/test_qc.R tests/testthat/test_qc_pipe_epic.R tests/testthat/test_read_is_annotated.R tests/testthat/test_read_set_annotation_epic_v2.R tests/testthat/test_utils.R vignettes/beadchip.Rmd