Index

Symbols

--version pymethyl-install command line option pymethyl-preprocess command line option pymethyl-utils command line option pymethyl-visualize command line option -a, --algorithm <algorithm> pymethyl-utils-ref_estimate_cell_counts command line option -a, --annot pymethyl-visualize-plot_heatmap command line option -a, --array_type <array_type> pymethyl-utils-print_number_sex_cpgs command line option pymethyl-utils-remove_sex command line option pymethyl-utils-remove_snps command line option -a, --axes_off pymethyl-visualize-transform_plot command line option -a, --axis <axis> pymethyl-utils-concat_csv command line option -b, --basename_col <basename_col> pymethyl-preprocess-create_sample_sheet command line option -bnc, --p_beadnum_cpgs <p_beadnum_cpgs> pymethyl-preprocess-preprocess_pipeline command line option -bns, --p_beadnum_samples <p_beadnum_samples> pymethyl-preprocess-preprocess_pipeline command line option -c, --chunk_size <chunk_size> pymethyl-preprocess-batch_deploy_preprocess command line option -c, --cluster pymethyl-visualize-plot_heatmap command line option -c, --col <col> pymethyl-utils-bin_column command line option pymethyl-utils-pkl_to_csv command line option -c, --column_of_interest <column_of_interest> pymethyl-visualize-transform_plot command line option -c, --cpg_pkl <cpg_pkl> pymethyl-utils-set_part_array_background command line option pymethyl-utils-subset_array command line option pymethyl-utils-write_cpgs command line option -c, --cpg_replace_method <cpg_replace_method> pymethyl-utils-create_external_validation_set command line option -c, --include_columns_file <include_columns_file> pymethyl-preprocess-create_sample_sheet command line option -c, --index_col <index_col> pymethyl-utils-overwrite_pheno_data command line option -cat, --categorical pymethyl-utils-train_test_val_split command line option -cc, --case_control_override pymethyl-visualize-transform_plot command line option -col, --color_column <color_column> pymethyl-visualize-plot_heatmap command line option -cols, --plot_cols <plot_cols> pymethyl-visualize-plot_cell_type_results command line option -ct, --cpg_threshold <cpg_threshold> pymethyl-preprocess-imputation_pipeline command line option -d, --disease_class_column <disease_class_column> pymethyl-preprocess-create_sample_sheet command line option -d, --disease_only pymethyl-preprocess-get_categorical_distribution command line option pymethyl-preprocess-imputation_pipeline command line option pymethyl-preprocess-remove_diseases command line option pymethyl-preprocess-split_preprocess_input_by_subtype command line option pymethyl-utils-fix_key command line option -d, --min_dist <min_dist> pymethyl-visualize-transform_plot command line option -d, --optional_input_pkl_dir <optional_input_pkl_dir> pymethyl-preprocess-combine_methylation_arrays command line option -d, --second_sheet_disease pymethyl-preprocess-merge_sample_sheets command line option -do, --disease_only pymethyl-utils-train_test_val_split command line option -e, --exclude <exclude> pymethyl-preprocess-combine_methylation_arrays command line option -e, --exclude_disease_list <exclude_disease_list> pymethyl-preprocess-remove_diseases command line option -f, --feature_selection_method <feature_selection_method> pymethyl-preprocess-feature_select command line option pymethyl-preprocess-imputation_pipeline command line option pymethyl-utils-feature_select_train_val_test command line option -fs, --font_scale <font_scale> pymethyl-visualize-plot_cell_type_results command line option pymethyl-visualize-plot_heatmap command line option -g, --geo_query <geo_query> pymethyl-preprocess-download_geo command line option -i, --idat_csv <idat_csv> pymethyl-preprocess-split_preprocess_input_by_subtype command line option -i, --idat_dir <idat_dir> pymethyl-preprocess-create_sample_sheet command line option pymethyl-preprocess-preprocess_pipeline command line option -i, --input_csv <input_csv> pymethyl-visualize-plot_cell_type_results command line option pymethyl-visualize-plot_heatmap command line option -i, --input_dir <input_dir> pymethyl-utils-move_jpg command line option -i, --input_pkl <input_pkl> pymethyl-preprocess-feature_select command line option pymethyl-preprocess-imputation_pipeline command line option pymethyl-preprocess-na_report command line option pymethyl-utils-backup_pkl command line option pymethyl-utils-counts command line option pymethyl-utils-fix_key command line option pymethyl-utils-modify_pheno_data command line option pymethyl-utils-overwrite_pheno_data command line option pymethyl-utils-pkl_to_csv command line option pymethyl-utils-print_number_sex_cpgs command line option pymethyl-utils-print_shape command line option pymethyl-utils-remove_sex command line option pymethyl-utils-remove_snps command line option pymethyl-utils-set_part_array_background command line option pymethyl-utils-stratify command line option pymethyl-utils-subset_array command line option pymethyl-utils-train_test_val_split command line option pymethyl-utils-write_cpgs command line option pymethyl-visualize-transform_plot command line option -i, --input_pkl_dir <input_pkl_dir> pymethyl-utils-feature_select_train_val_test command line option -i, --input_pkls <input_pkls> pymethyl-preprocess-combine_methylation_arrays command line option -i, --subtype_output_dir <subtype_output_dir> pymethyl-preprocess-batch_deploy_preprocess command line option -i1, --input_csv <input_csv> pymethyl-utils-concat_csv command line option -i2, --input_csv2 <input_csv2> pymethyl-utils-concat_csv command line option -idx, --index_col <index_col> pymethyl-visualize-plot_heatmap command line option -is, --formatted_sample_sheet <formatted_sample_sheet> pymethyl-preprocess-get_categorical_distribution command line option pymethyl-preprocess-remove_diseases command line option -is, --input_formatted_sample_sheet <input_formatted_sample_sheet> pymethyl-utils-modify_pheno_data command line option pymethyl-utils-overwrite_pheno_data command line option -is, --input_sample_sheet <input_sample_sheet> pymethyl-preprocess-create_sample_sheet command line option pymethyl-preprocess-meffil_encode command line option -k, --key <key> pymethyl-preprocess-get_categorical_distribution command line option pymethyl-utils-counts command line option pymethyl-utils-fix_key command line option pymethyl-utils-stratify command line option pymethyl-utils-train_test_val_split command line option -k, --n_neighbors <n_neighbors> pymethyl-preprocess-imputation_pipeline command line option -l, --header_line <header_line> pymethyl-preprocess-create_sample_sheet command line option -l, --library <library> pymethyl-utils-ref_estimate_cell_counts command line option -l, --low_count <low_count> pymethyl-preprocess-remove_diseases command line option -m, --mad_top_cpgs <mad_top_cpgs> pymethyl-preprocess-feature_select command line option pymethyl-utils-feature_select_train_val_test command line option -m, --manager pymethyl-install-install_custom command line option -m, --mapping_file <mapping_file> pymethyl-preprocess-create_sample_sheet command line option -m, --matrix_type <matrix_type> pymethyl-visualize-plot_heatmap command line option

-m, --meffil pymethyl-preprocess-batch_deploy_preprocess command line option pymethyl-preprocess-preprocess_pipeline command line option -m, --method <method> pymethyl-preprocess-imputation_pipeline command line option -m, --metric <metric> pymethyl-visualize-transform_plot command line option -max, --max_val <max_val> pymethyl-visualize-plot_heatmap command line option -min, --min_val <min_val> pymethyl-visualize-plot_heatmap command line option -mm, --metric <metric> pymethyl-preprocess-feature_select command line option pymethyl-preprocess-imputation_pipeline command line option pymethyl-utils-feature_select_train_val_test command line option -n, --n_bins <n_bins> pymethyl-utils-bin_column command line option -n, --n_cores <n_cores> pymethyl-preprocess-batch_deploy_preprocess command line option pymethyl-preprocess-preprocess_pipeline command line option -n, --n_top_cpgs <n_top_cpgs> pymethyl-preprocess-feature_select command line option pymethyl-preprocess-imputation_pipeline command line option pymethyl-utils-feature_select_train_val_test command line option -n, --norm pymethyl-visualize-plot_heatmap command line option -nd, --no_disease_merge pymethyl-preprocess-merge_sample_sheets command line option -nfs, --n_neighbors_fs <n_neighbors_fs> pymethyl-preprocess-imputation_pipeline command line option -nn, --n_neighbors <n_neighbors> pymethyl-preprocess-feature_select command line option pymethyl-utils-feature_select_train_val_test command line option pymethyl-visualize-transform_plot command line option -noob, --noob_norm pymethyl-preprocess-preprocess_pipeline command line option -o, --outfilename <outfilename> pymethyl-visualize-plot_cell_type_results command line option pymethyl-visualize-plot_heatmap command line option -o, --output_csv <output_csv> pymethyl-utils-concat_csv command line option pymethyl-utils-ref_estimate_cell_counts command line option -o, --output_dir <output_dir> pymethyl-preprocess-download_clinical command line option pymethyl-preprocess-download_geo command line option pymethyl-preprocess-download_tcga command line option pymethyl-preprocess-na_report command line option pymethyl-utils-feature_select_train_val_test command line option pymethyl-utils-move_jpg command line option pymethyl-utils-pkl_to_csv command line option pymethyl-utils-stratify command line option pymethyl-utils-train_test_val_split command line option -o, --output_file <output_file> pymethyl-visualize-transform_plot command line option -o, --output_pkl <output_pkl> pymethyl-preprocess-combine_methylation_arrays command line option pymethyl-preprocess-feature_select command line option pymethyl-preprocess-imputation_pipeline command line option pymethyl-preprocess-preprocess_pipeline command line option pymethyl-utils-backup_pkl command line option pymethyl-utils-create_external_validation_set command line option pymethyl-utils-fix_key command line option pymethyl-utils-modify_pheno_data command line option pymethyl-utils-overwrite_pheno_data command line option pymethyl-utils-remove_sex command line option pymethyl-utils-remove_snps command line option pymethyl-utils-set_part_array_background command line option pymethyl-utils-subset_array command line option -o, --subtype_output_dir <subtype_output_dir> pymethyl-preprocess-split_preprocess_input_by_subtype command line option -os, --output_sample_sheet <output_sample_sheet> pymethyl-preprocess-concat_sample_sheets command line option pymethyl-preprocess-create_sample_sheet command line option pymethyl-preprocess-meffil_encode command line option pymethyl-preprocess-merge_sample_sheets command line option -os, --output_sheet_name <output_sheet_name> pymethyl-preprocess-remove_diseases command line option -ot, --output_test_pkl <output_test_pkl> pymethyl-utils-bin_column command line option -p, --package <package> pymethyl-install-install_custom command line option pymethyl-install-install_r_packages command line option -p, --pc_qc_parameters_csv <pc_qc_parameters_csv> pymethyl-preprocess-batch_deploy_preprocess command line option -p, --pipeline <pipeline> pymethyl-preprocess-preprocess_pipeline command line option -pc, --n_pcs <n_pcs> pymethyl-preprocess-preprocess_pipeline command line option -pdc, --p_detection_cpgs <p_detection_cpgs> pymethyl-preprocess-preprocess_pipeline command line option -pds, --p_detection_samples <p_detection_samples> pymethyl-preprocess-preprocess_pipeline command line option -q, --query_pkl <query_pkl> pymethyl-utils-create_external_validation_set command line option -qc, --qc_only pymethyl-preprocess-batch_deploy_preprocess command line option pymethyl-preprocess-preprocess_pipeline command line option -r, --head_directory pymethyl-preprocess-na_report command line option -r, --orientation <orientation> pymethyl-preprocess-imputation_pipeline command line option -r, --run pymethyl-preprocess-batch_deploy_preprocess command line option -ref, --reference <reference> pymethyl-utils-ref_estimate_cell_counts command line option -ro, --input_r_object_dir <input_r_object_dir> pymethyl-utils-ref_estimate_cell_counts command line option -s, --series pymethyl-preprocess-batch_deploy_preprocess command line option -s, --solver <solver> pymethyl-preprocess-imputation_pipeline command line option -s, --source_type <source_type> pymethyl-preprocess-create_sample_sheet command line option -s, --supervised pymethyl-visualize-transform_plot command line option -s1, --sample_sheet1 <sample_sheet1> pymethyl-preprocess-concat_sample_sheets command line option pymethyl-preprocess-merge_sample_sheets command line option -s2, --sample_sheet2 <sample_sheet2> pymethyl-preprocess-concat_sample_sheets command line option pymethyl-preprocess-merge_sample_sheets command line option -sc, --sex_cutoff <sex_cutoff> pymethyl-preprocess-preprocess_pipeline command line option -sd, --sex_sd <sex_sd> pymethyl-preprocess-preprocess_pipeline command line option -sd, --subtype_delimiter <subtype_delimiter> pymethyl-preprocess-get_categorical_distribution command line option pymethyl-preprocess-imputation_pipeline command line option pymethyl-preprocess-remove_diseases command line option pymethyl-preprocess-split_preprocess_input_by_subtype command line option pymethyl-utils-fix_key command line option pymethyl-utils-train_test_val_split command line option -ss, --split_by_subtype pymethyl-preprocess-imputation_pipeline command line option -st, --sample_threshold <sample_threshold> pymethyl-preprocess-imputation_pipeline command line option -t, --test_pkl <test_pkl> pymethyl-utils-bin_column command line option -t, --torque pymethyl-preprocess-batch_deploy_preprocess command line option -t, --train_pkl <train_pkl> pymethyl-utils-create_external_validation_set command line option -t, --transpose pymethyl-visualize-plot_heatmap command line option -tp, --train_percent <train_percent> pymethyl-utils-train_test_val_split command line option -u, --use_cache pymethyl-preprocess-batch_deploy_preprocess command line option pymethyl-preprocess-preprocess_pipeline command line option -vp, --val_percent <val_percent> pymethyl-utils-train_test_val_split command line option -x, --xticks pymethyl-visualize-plot_heatmap command line option -y, --yticks pymethyl-visualize-plot_heatmap command line option

A

assign_results_to_pheno_col() (pymethylprocess.general_machine_learning.MachineLearning method)

B

bin_column() (pymethylprocess.MethylationDataTypes.MethylationArray method)

C

categorical_breakdown() (pymethylprocess.MethylationDataTypes.MethylationArray method)

combine() (pymethylprocess.MethylationDataTypes.MethylationArrays method) concat() (pymethylprocess.PreProcessDataTypes.PreProcessPhenoData method)

D

download_clinical() (pymethylprocess.PreProcessDataTypes.TCGADownloader method)

download_geo() (pymethylprocess.PreProcessDataTypes.TCGADownloader method) download_tcga() (pymethylprocess.PreProcessDataTypes.TCGADownloader method)

E

est_cell_counts_IDOL() (in module pymethylprocess.meffil_functions) est_cell_counts_meffil() (in module pymethylprocess.meffil_functions) est_cell_counts_minfi() (in module pymethylprocess.meffil_functions) export() (pymethylprocess.PreProcessDataTypes.PreProcessPhenoData method) export_csv() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) export_pickle() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method)

export_sql() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) extract_manifest() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) extract_pheno_beta_df_from_folder() (in module pymethylprocess.MethylationDataTypes) extract_pheno_beta_df_from_pickle_dict() (in module pymethylprocess.MethylationDataTypes) extract_pheno_beta_df_from_sql() (in module pymethylprocess.MethylationDataTypes) extract_pheno_data() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method)

F

feature_select() (pymethylprocess.MethylationDataTypes.MethylationArray method) filter_beta() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) fit() (pymethylprocess.general_machine_learning.MachineLearning method) fit_predict() (pymethylprocess.general_machine_learning.MachineLearning method)

fit_transform() (pymethylprocess.general_machine_learning.MachineLearning method) format_custom() (pymethylprocess.PreProcessDataTypes.PreProcessPhenoData method) format_geo() (pymethylprocess.PreProcessDataTypes.PreProcessPhenoData method) format_tcga() (pymethylprocess.PreProcessDataTypes.PreProcessPhenoData method) from_pickle() (pymethylprocess.MethylationDataTypes.MethylationArray class method)

G

get_beta() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) get_categorical_distribution() (pymethylprocess.PreProcessDataTypes.PreProcessPhenoData method)

get_meth() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) get_unmeth() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) groupby() (pymethylprocess.MethylationDataTypes.MethylationArray method)

I

impute() (pymethylprocess.MethylationDataTypes.MethylationArray method) (pymethylprocess.MethylationDataTypes.MethylationArrays method)

ImputerObject (class in pymethylprocess.MethylationDataTypes)

L

load_detection_p_values_beadnum() (in module pymethylprocess.meffil_functions)

load_idats() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method)

M

MachineLearning (class in pymethylprocess.general_machine_learning) merge() (pymethylprocess.PreProcessDataTypes.PreProcessPhenoData method) merge_preprocess_sheet() (pymethylprocess.MethylationDataTypes.MethylationArray method)

MethylationArray (class in pymethylprocess.MethylationDataTypes) MethylationArrays (class in pymethylprocess.MethylationDataTypes) move_jpg() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method)

O

output_pheno_beta() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method)

overwrite_pheno_data() (pymethylprocess.MethylationDataTypes.MethylationArray method)

P

plot_original_qc() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) plot_qc_metrics() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) predict() (pymethylprocess.general_machine_learning.MachineLearning method) preprocess_enmix_pipeline() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) preprocessENmix() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) PreProcessIDAT (class in pymethylprocess.PreProcessDataTypes) preprocessMeffil() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) preprocessNoob() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) PreProcessPhenoData (class in pymethylprocess.PreProcessDataTypes) preprocessRAW() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) pymethyl-install command line option --version pymethyl-install-install_custom command line option -m, --manager -p, --package <package> pymethyl-install-install_r_packages command line option -p, --package <package> pymethyl-preprocess command line option --version pymethyl-preprocess-batch_deploy_preprocess command line option -c, --chunk_size <chunk_size> -i, --subtype_output_dir <subtype_output_dir> -m, --meffil -n, --n_cores <n_cores> -p, --pc_qc_parameters_csv <pc_qc_parameters_csv> -qc, --qc_only -r, --run -s, --series -t, --torque -u, --use_cache pymethyl-preprocess-combine_methylation_arrays command line option -d, --optional_input_pkl_dir <optional_input_pkl_dir> -e, --exclude <exclude> -i, --input_pkls <input_pkls> -o, --output_pkl <output_pkl> pymethyl-preprocess-concat_sample_sheets command line option -os, --output_sample_sheet <output_sample_sheet> -s1, --sample_sheet1 <sample_sheet1> -s2, --sample_sheet2 <sample_sheet2> pymethyl-preprocess-create_sample_sheet command line option -b, --basename_col <basename_col> -c, --include_columns_file <include_columns_file> -d, --disease_class_column <disease_class_column> -i, --idat_dir <idat_dir> -is, --input_sample_sheet <input_sample_sheet> -l, --header_line <header_line> -m, --mapping_file <mapping_file> -os, --output_sample_sheet <output_sample_sheet> -s, --source_type <source_type> pymethyl-preprocess-download_clinical command line option -o, --output_dir <output_dir> pymethyl-preprocess-download_geo command line option -g, --geo_query <geo_query> -o, --output_dir <output_dir> pymethyl-preprocess-download_tcga command line option -o, --output_dir <output_dir> pymethyl-preprocess-feature_select command line option -f, --feature_selection_method <feature_selection_method> -i, --input_pkl <input_pkl> -m, --mad_top_cpgs <mad_top_cpgs> -mm, --metric <metric> -n, --n_top_cpgs <n_top_cpgs> -nn, --n_neighbors <n_neighbors> -o, --output_pkl <output_pkl> pymethyl-preprocess-get_categorical_distribution command line option -d, --disease_only -is, --formatted_sample_sheet <formatted_sample_sheet> -k, --key <key> -sd, --subtype_delimiter <subtype_delimiter> pymethyl-preprocess-imputation_pipeline command line option -ct, --cpg_threshold <cpg_threshold> -d, --disease_only -f, --feature_selection_method <feature_selection_method> -i, --input_pkl <input_pkl> -k, --n_neighbors <n_neighbors> -m, --method <method> -mm, --metric <metric> -n, --n_top_cpgs <n_top_cpgs> -nfs, --n_neighbors_fs <n_neighbors_fs> -o, --output_pkl <output_pkl> -r, --orientation <orientation> -s, --solver <solver> -sd, --subtype_delimiter <subtype_delimiter> -ss, --split_by_subtype -st, --sample_threshold <sample_threshold> pymethyl-preprocess-meffil_encode command line option -is, --input_sample_sheet <input_sample_sheet> -os, --output_sample_sheet <output_sample_sheet> pymethyl-preprocess-merge_sample_sheets command line option -d, --second_sheet_disease -nd, --no_disease_merge -os, --output_sample_sheet <output_sample_sheet> -s1, --sample_sheet1 <sample_sheet1> -s2, --sample_sheet2 <sample_sheet2> pymethyl-preprocess-na_report command line option -i, --input_pkl <input_pkl> -o, --output_dir <output_dir> -r, --head_directory pymethyl-preprocess-preprocess_pipeline command line option -bnc, --p_beadnum_cpgs <p_beadnum_cpgs> -bns, --p_beadnum_samples <p_beadnum_samples> -i, --idat_dir <idat_dir> -m, --meffil -n, --n_cores <n_cores> -noob, --noob_norm -o, --output_pkl <output_pkl> -p, --pipeline <pipeline> -pc, --n_pcs <n_pcs> -pdc, --p_detection_cpgs <p_detection_cpgs> -pds, --p_detection_samples <p_detection_samples> -qc, --qc_only -sc, --sex_cutoff <sex_cutoff> -sd, --sex_sd <sex_sd> -u, --use_cache pymethyl-preprocess-remove_diseases command line option -d, --disease_only -e, --exclude_disease_list <exclude_disease_list> -is, --formatted_sample_sheet <formatted_sample_sheet> -l, --low_count <low_count> -os, --output_sheet_name <output_sheet_name> -sd, --subtype_delimiter <subtype_delimiter> pymethyl-preprocess-split_preprocess_input_by_subtype command line option -d, --disease_only -i, --idat_csv <idat_csv> -o, --subtype_output_dir <subtype_output_dir> -sd, --subtype_delimiter <subtype_delimiter> pymethyl-utils command line option --version pymethyl-utils-backup_pkl command line option -i, --input_pkl <input_pkl> -o, --output_pkl <output_pkl>

pymethyl-utils-bin_column command line option -c, --col <col> -n, --n_bins <n_bins> -ot, --output_test_pkl <output_test_pkl> -t, --test_pkl <test_pkl> pymethyl-utils-concat_csv command line option -a, --axis <axis> -i1, --input_csv <input_csv> -i2, --input_csv2 <input_csv2> -o, --output_csv <output_csv> pymethyl-utils-counts command line option -i, --input_pkl <input_pkl> -k, --key <key> pymethyl-utils-create_external_validation_set command line option -c, --cpg_replace_method <cpg_replace_method> -o, --output_pkl <output_pkl> -q, --query_pkl <query_pkl> -t, --train_pkl <train_pkl> pymethyl-utils-feature_select_train_val_test command line option -f, --feature_selection_method <feature_selection_method> -i, --input_pkl_dir <input_pkl_dir> -m, --mad_top_cpgs <mad_top_cpgs> -mm, --metric <metric> -n, --n_top_cpgs <n_top_cpgs> -nn, --n_neighbors <n_neighbors> -o, --output_dir <output_dir> pymethyl-utils-fix_key command line option -d, --disease_only -i, --input_pkl <input_pkl> -k, --key <key> -o, --output_pkl <output_pkl> -sd, --subtype_delimiter <subtype_delimiter> pymethyl-utils-modify_pheno_data command line option -i, --input_pkl <input_pkl> -is, --input_formatted_sample_sheet <input_formatted_sample_sheet> -o, --output_pkl <output_pkl> pymethyl-utils-move_jpg command line option -i, --input_dir <input_dir> -o, --output_dir <output_dir> pymethyl-utils-overwrite_pheno_data command line option -c, --index_col <index_col> -i, --input_pkl <input_pkl> -is, --input_formatted_sample_sheet <input_formatted_sample_sheet> -o, --output_pkl <output_pkl> pymethyl-utils-pkl_to_csv command line option -c, --col <col> -i, --input_pkl <input_pkl> -o, --output_dir <output_dir> pymethyl-utils-print_number_sex_cpgs command line option -a, --array_type <array_type> -i, --input_pkl <input_pkl> pymethyl-utils-print_shape command line option -i, --input_pkl <input_pkl> pymethyl-utils-ref_estimate_cell_counts command line option -a, --algorithm <algorithm> -l, --library <library> -o, --output_csv <output_csv> -ref, --reference <reference> -ro, --input_r_object_dir <input_r_object_dir> pymethyl-utils-remove_sex command line option -a, --array_type <array_type> -i, --input_pkl <input_pkl> -o, --output_pkl <output_pkl> pymethyl-utils-remove_snps command line option -a, --array_type <array_type> -i, --input_pkl <input_pkl> -o, --output_pkl <output_pkl> pymethyl-utils-set_part_array_background command line option -c, --cpg_pkl <cpg_pkl> -i, --input_pkl <input_pkl> -o, --output_pkl <output_pkl> pymethyl-utils-stratify command line option -i, --input_pkl <input_pkl> -k, --key <key> -o, --output_dir <output_dir> pymethyl-utils-subset_array command line option -c, --cpg_pkl <cpg_pkl> -i, --input_pkl <input_pkl> -o, --output_pkl <output_pkl> pymethyl-utils-train_test_val_split command line option -cat, --categorical -do, --disease_only -i, --input_pkl <input_pkl> -k, --key <key> -o, --output_dir <output_dir> -sd, --subtype_delimiter <subtype_delimiter> -tp, --train_percent <train_percent> -vp, --val_percent <val_percent> pymethyl-utils-write_cpgs command line option -c, --cpg_pkl <cpg_pkl> -i, --input_pkl <input_pkl> pymethyl-visualize command line option --version pymethyl-visualize-plot_cell_type_results command line option -cols, --plot_cols <plot_cols> -fs, --font_scale <font_scale> -i, --input_csv <input_csv> -o, --outfilename <outfilename> pymethyl-visualize-plot_heatmap command line option -a, --annot -c, --cluster -col, --color_column <color_column> -fs, --font_scale <font_scale> -i, --input_csv <input_csv> -idx, --index_col <index_col> -m, --matrix_type <matrix_type> -max, --max_val <max_val> -min, --min_val <min_val> -n, --norm -o, --outfilename <outfilename> -t, --transpose -x, --xticks -y, --yticks pymethyl-visualize-transform_plot command line option -a, --axes_off -c, --column_of_interest <column_of_interest> -cc, --case_control_override -d, --min_dist <min_dist> -i, --input_pkl <input_pkl> -m, --metric <metric> -nn, --n_neighbors <n_neighbors> -o, --output_file <output_file> -s, --supervised pymethylprocess.general_machine_learning (module) pymethylprocess.meffil_functions (module) pymethylprocess.MethylationDataTypes (module) pymethylprocess.PreProcessDataTypes (module)

R

r_autosomal_cpgs() (in module pymethylprocess.meffil_functions) r_snp_cpgs() (in module pymethylprocess.meffil_functions) remove_diseases() (pymethylprocess.PreProcessDataTypes.PreProcessPhenoData method) remove_missingness() (pymethylprocess.MethylationDataTypes.MethylationArray method) remove_na_samples() (pymethylprocess.MethylationDataTypes.MethylationArray method) remove_sex() (in module pymethylprocess.meffil_functions) remove_whitespace() (pymethylprocess.MethylationDataTypes.MethylationArray method)

return_beta() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method) return_cpgs() (pymethylprocess.MethylationDataTypes.MethylationArray method) return_idx() (pymethylprocess.MethylationDataTypes.MethylationArray method) return_imputer() (pymethylprocess.MethylationDataTypes.ImputerObject method) return_outcome_metric() (pymethylprocess.general_machine_learning.MachineLearning method) return_raw_beta_array() (pymethylprocess.MethylationDataTypes.MethylationArray method) return_shape() (pymethylprocess.MethylationDataTypes.MethylationArray method)

S

set_missing() (in module pymethylprocess.meffil_functions) split_by_subtype() (pymethylprocess.MethylationDataTypes.MethylationArray method) split_key() (pymethylprocess.MethylationDataTypes.MethylationArray method) (pymethylprocess.PreProcessDataTypes.PreProcessPhenoData method)

split_train_test() (pymethylprocess.MethylationDataTypes.MethylationArray method) store_results() (pymethylprocess.general_machine_learning.MachineLearning method) subsample() (pymethylprocess.MethylationDataTypes.MethylationArray method) subset_cpgs() (pymethylprocess.MethylationDataTypes.MethylationArray method) subset_index() (pymethylprocess.MethylationDataTypes.MethylationArray method)

T

TCGADownloader (class in pymethylprocess.PreProcessDataTypes) to_methyl_array() (pymethylprocess.PreProcessDataTypes.PreProcessIDAT method)

transform() (pymethylprocess.general_machine_learning.MachineLearning method) transform_results_to_beta() (pymethylprocess.general_machine_learning.MachineLearning method)

W

write_csvs() (pymethylprocess.MethylationDataTypes.MethylationArray method) write_db() (pymethylprocess.MethylationDataTypes.MethylationArray method)

write_dbs() (pymethylprocess.MethylationDataTypes.MethylationArrays method) write_pickle() (pymethylprocess.MethylationDataTypes.MethylationArray method) write_pkls() (pymethylprocess.MethylationDataTypes.MethylationArrays method)