Index

A

add_bar() (pymaftools.plot.OncoPlot.OncoPlot method) add_cmap() (pymaftools.plot.ColorManager.ColorManager method) add_exon_size() (pymaftools.core.PivotTable.PivotTable method) add_feature_annotation() (pymaftools.plot.OncoPlot.OncoPlot method) add_feature_metadata() (pymaftools.core.PivotTable.PivotTable method) add_freq() (pymaftools.core.PivotTable.PivotTable method) (pymaftools.plot.OncoPlot.OncoPlot method) add_legend() (pymaftools.plot.BasePlot.BasePlot method) (pymaftools.plot.LegendManager.LegendManager method) add_numeric_colorbar() (pymaftools.plot.LegendManager.LegendManager method) add_numeric_legend() (pymaftools.plot.LegendManager.LegendManager method) add_sample_annotation() (pymaftools.plot.OncoPlot.OncoPlot method) add_sample_metadata() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method)

add_shape_legend() (pymaftools.plot.LegendManager.LegendManager method) add_table() (pymaftools.core.Cohort.Cohort method) add_track() (pymaftools.plot.OncoPlot.OncoPlot method) add_xticklabel() (pymaftools.plot.OncoPlot.OncoPlot method) adjust_color_brightness() (pymaftools.plot.ColorManager.ColorManager method) align_cases() (pymaftools.io.tcga.GDCClient method) align_cluster_label_dict() (in module pymaftools.core.Clustering) align_clusters() (in module pymaftools.core.Clustering) align_manifests() (pymaftools.io.tcga.GDCClient method) align_multi_project() (pymaftools.io.tcga.GDCClient method) ALL_MUTATION_CMAP (pymaftools.plot.ColorManager.ColorManager attribute) alt (pymaftools.io.vcf.record.VCFRecord attribute) analyze_similarity() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) apply_cmap_to_data() (pymaftools.plot.ColorManager.ColorManager method) ASCStackingModel (class in pymaftools.model.StackingModel)

B

band_ratio() (pymaftools.plot.CopyNumberVariationTablePlot.CopyNumberVariationTablePlot method) BarTrack (class in pymaftools.plot.Track) BasePlot (class in pymaftools.plot.BasePlot) build() (pymaftools.io.tcga.TCGAClinicalBuilder method) (pymaftools.io.tcga.TCGACNVSegmentBuilder method) (pymaftools.io.tcga.TCGAMutationBuilder method) (pymaftools.io.tcga.TCGATableBuilder method)

build_cytoband_table() (pymaftools.io.tcga.TCGACNVSegmentBuilder method) build_file_mapping() (pymaftools.io.tcga.GDCClient method) build_model() (pymaftools.model.StackingModel.OmicsStackingModel method) build_sample_metadata() (pymaftools.io.tcga.TCGAMutationBuilder method) (pymaftools.io.tcga.TCGATableBuilder method)

C

calculate_ari_matrix() (in module pymaftools.core.Clustering) calculate_feature_frequency() (pymaftools.core.PivotTable.PivotTable method) calculate_group_similarity_pvalues() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) calculate_TMB() (pymaftools.core.PivotTable.PivotTable method) calculate_tmb() (pymaftools.core.PivotTable.PivotTable method) caller (pymaftools.io.vcf.record.VCFRecord attribute) CancerCellFractionTable (class in pymaftools.core.CancerCellFractionTable) capture_size() (in module pymaftools.core.PivotTable) categorical_heatmap() (pymaftools.plot.OncoPlot.OncoPlot static method) CategoricalTrack (class in pymaftools.plot.Track) change_index_level() (pymaftools.core.MAF.MAF method) chrom (pymaftools.io.vcf.record.VCFRecord attribute) clear_legends() (pymaftools.plot.BasePlot.BasePlot method) (pymaftools.plot.LegendManager.LegendManager method) close() (pymaftools.plot.BasePlot.BasePlot method) CNV_CMAP (pymaftools.plot.ColorManager.ColorManager attribute)

Cohort (class in pymaftools.core.Cohort) colorbar_legend() (pymaftools.plot.Track.NumericTrack method) ColorManager (class in pymaftools.plot.ColorManager) compare_group_pairs() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) compute_similarity() (pymaftools.core.PivotTable.PivotTable method) confusion_matrix() (pymaftools.model.StackingModel.OmicsStackingModel method) convert_ndarray_to_list() (in module pymaftools.core.Clustering) CooccurrenceMatrix (class in pymaftools.core.PairwiseMatrix) copy() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method) CopyNumberVariationTable (class in pymaftools.core.CopyNumberVariationTable) CopyNumberVariationTablePlot (class in pymaftools.plot.CopyNumberVariationTablePlot) count_legends() (pymaftools.plot.LegendManager.LegendManager method) create_from_dict() (pymaftools.plot.LegendManager.LegendManager static method) create_matplotlib_cmap() (pymaftools.plot.ColorManager.ColorManager method) cross_validate_importance() (in module pymaftools.model.modelUtils)

D

decode_y() (pymaftools.model.StackingModel.OmicsStackingModel method) default_oncoplot() (pymaftools.plot.OncoPlot.OncoPlot static method) deseq2() (pymaftools.core.ExpressionTable.ExpressionTable method)

download() (pymaftools.io.tcga.GDCClient method) draw_categorical_heatmap() (in module pymaftools.plot.Track) draw_colorbar() (pymaftools.plot.Track.NumericMatrixTrack method) draw_cube() (pymaftools.plot.MethodsPlot.MethodsPlot static method)

E

encode_y() (pymaftools.model.StackingModel.OmicsStackingModel method) ensembl_to_symbol() (in module pymaftools.utils.geneinfo) entry_equal_properties() (pymaftools.plot.FontManager.FontManager method)

evaluate() (pymaftools.model.StackingModel.OmicsStackingModel method) evaluate_model() (in module pymaftools.model.modelUtils) ExpressionTable (class in pymaftools.core.ExpressionTable) ExpressionTablePlot (class in pymaftools.plot.ExpressionTablePlot)

F

feature_metadata (pymaftools.core.PivotTable.PivotTable attribute) fetch_clinical_table() (pymaftools.io.tcga.GDCClient method) fetch_msigdb_geneset() (in module pymaftools.utils.geneset) file_pattern (pymaftools.io.tcga.TCGACNVGeneBuilder attribute) (pymaftools.io.tcga.TCGACNVSegmentBuilder attribute) (pymaftools.io.tcga.TCGAExpressionBuilder attribute) (pymaftools.io.tcga.TCGAMethylationBuilder attribute) (pymaftools.io.tcga.TCGAMutationBuilder attribute) (pymaftools.io.tcga.TCGATableBuilder attribute) filter (pymaftools.io.vcf.record.VCFRecord attribute) filter_by_freq() (pymaftools.core.PivotTable.PivotTable method) filter_by_statistical_test() (pymaftools.core.PivotTable.PivotTable method) filter_by_variance() (pymaftools.core.PivotTable.PivotTable method) filter_low_expression() (pymaftools.core.ExpressionTable.ExpressionTable method)

filter_maf() (pymaftools.core.MAF.MAF method) filter_variants() (pymaftools.core.VCF.VCF method) find_deg() (pymaftools.core.ExpressionTable.ExpressionTable method) fit() (pymaftools.model.StackingModel.OmicsStackingModel method) fit_transform() (pymaftools.utils.reduction.PCA_CCA method) FontManager (class in pymaftools.plot.FontManager) FreqTrack (class in pymaftools.plot.Track) from_anndata() (pymaftools.core.PivotTable.PivotTable class method) from_config() (pymaftools.io.tcga.GDCClient class method) from_file() (pymaftools.core.VCF.VCF class method) from_pivot_table() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable class method) FUNCTIONAL_CMAP (pymaftools.plot.ColorManager.ColorManager attribute) FUNCTIONAL_GROUP (pymaftools.plot.ColorManager.ColorManager attribute) FUNCTIONAL_ORDER (pymaftools.plot.ColorManager.ColorManager attribute)

G

GDCClient (class in pymaftools.io.tcga) generate_categorical_cmap() (pymaftools.plot.ColorManager.ColorManager method) generate_cmap_from_list() (pymaftools.plot.ColorManager.ColorManager method) generate_full_manifests() (pymaftools.io.tcga.GDCClient method) generate_manifests() (pymaftools.io.tcga.GDCClient method) generate_permutation_list() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) get_available_fonts() (pymaftools.plot.FontManager.FontManager method) get_cases() (pymaftools.io.tcga.GDCClient method) get_cmap() (pymaftools.plot.ColorManager.ColorManager method) get_color_manager() (pymaftools.plot.BasePlot.BasePlot method) get_domain_info() (pymaftools.core.MAF.MAF static method) get_exon_size() (in module pymaftools.utils.geneinfo) get_file_metadata() (pymaftools.io.tcga.GDCClient method) get_gene_description_df() (in module pymaftools.utils.geneinfo) get_gene_info_json() (in module pymaftools.utils.geneinfo) get_importance() (in module pymaftools.model.modelUtils)

get_legend_dict() (pymaftools.plot.LegendManager.LegendManager method) get_legend_info() (pymaftools.plot.LegendManager.LegendManager method) get_legend_manager() (pymaftools.plot.BasePlot.BasePlot method) get_legend_names() (pymaftools.plot.BasePlot.BasePlot method) (pymaftools.plot.LegendManager.LegendManager method) get_mean_group_similarity() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) get_ncbi_gene_ID() (in module pymaftools.utils.geneinfo) get_ncbi_gene_IDs() (in module pymaftools.utils.geneinfo) get_omics_feature_importance() (pymaftools.model.StackingModel.OmicsStackingModel method) get_omics_weights() (pymaftools.model.StackingModel.OmicsStackingModel method) get_pair_values() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) get_pairs_subset() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) get_protein_info() (pymaftools.core.MAF.MAF method) get_target_sample_ID() (in module pymaftools.core.CopyNumberVariationTable) get_weights() (pymaftools.utils.reduction.PCA_CCA method) group_features() (pymaftools.plot.OncoPlot.OncoPlot method) group_samples() (pymaftools.plot.OncoPlot.OncoPlot method)

H

has_legend() (pymaftools.plot.BasePlot.BasePlot method) (pymaftools.plot.LegendManager.LegendManager method)

head() (pymaftools.core.PivotTable.PivotTable method) header (pymaftools.core.VCF.VCF attribute)

I

index_col (pymaftools.core.MAF.MAF attribute)

info() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method)

K

k_fold_clustering_evaluation() (in module pymaftools.core.Clustering)

L

label (pymaftools.plot.Track.NumericTrack property) legend_entries() (pymaftools.plot.Track.BarTrack method) (pymaftools.plot.Track.CategoricalTrack method) (pymaftools.plot.Track.MainMatrixTrack method) (pymaftools.plot.Track.Track method)

LegendManager (class in pymaftools.plot.LegendManager) load_ensembl_map() (in module pymaftools.utils.geneinfo) load_file_mapping() (in module pymaftools.io.tcga) load_gene_sizes() (in module pymaftools.utils.geneinfo) LollipopPlot (class in pymaftools.plot.LollipopPlot)

M

MAF (class in pymaftools.core.MAF) main() (pymaftools.plot.OncoPlot.OncoPlot method) MainMatrixTrack (class in pymaftools.plot.Track) merge() (pymaftools.core.PivotTable.PivotTable static method) merge_callers() (pymaftools.core.VCF.VCF class method) merge_mafs() (pymaftools.core.MAF.MAF static method) merge_mutations() (pymaftools.core.MAF.MAF static method) MethodsPlot (class in pymaftools.plot.MethodsPlot) ModelPlot (class in pymaftools.plot.ModelPlot) module pymaftools.core.CancerCellFractionTable pymaftools.core.Clustering pymaftools.core.Cohort pymaftools.core.CopyNumberVariationTable pymaftools.core.ExpressionTable pymaftools.core.MAF pymaftools.core.PairwiseMatrix pymaftools.core.PivotTable pymaftools.core.SignatureTable pymaftools.core.VCF pymaftools.io.tcga pymaftools.io.vcf.parsers pymaftools.io.vcf.record pymaftools.model.modelUtils pymaftools.model.StackingModel pymaftools.plot.BasePlot pymaftools.plot.ColorManager pymaftools.plot.CopyNumberVariationTablePlot pymaftools.plot.ExpressionTablePlot pymaftools.plot.FontManager pymaftools.plot.LegendManager pymaftools.plot.LollipopPlot pymaftools.plot.MethodsPlot pymaftools.plot.ModelPlot pymaftools.plot.OncoPlot pymaftools.plot.PivotStatsPlot pymaftools.plot.SignatureTablePlot pymaftools.plot.SmallVariationTablePlot pymaftools.plot.Track pymaftools.utils.geneinfo pymaftools.utils.geneset pymaftools.utils.reduction

mutation_enrichment_test() (pymaftools.core.PivotTable.PivotTable method) mutation_heatmap() (pymaftools.plot.OncoPlot.OncoPlot method) mutations_count (pymaftools.core.MAF.MAF property)

N

NONSYNONYMOUS_CMAP (pymaftools.plot.ColorManager.ColorManager attribute) nonsynonymous_types (pymaftools.core.MAF.MAF attribute) normal_ad (pymaftools.io.vcf.record.VCFRecord attribute) normal_dp (pymaftools.io.vcf.record.VCFRecord attribute)

normal_ref (pymaftools.io.vcf.record.VCFRecord attribute) normalize_weight() (pymaftools.plot.FontManager.FontManager static method) numeric_heatmap() (pymaftools.plot.OncoPlot.OncoPlot method) NumericMatrixTrack (class in pymaftools.plot.Track) NumericTrack (class in pymaftools.plot.Track)

O

OmicsStackingModel (class in pymaftools.model.StackingModel) OncoPlot (class in pymaftools.plot.OncoPlot)

oncoplot() (pymaftools.plot.PivotStatsPlot.PivotStatsPlot method) order() (pymaftools.core.PivotTable.PivotTable method)

P

paired_similarity_permutation_test() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) paired_similarity_utest() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) PairwiseMatrix (class in pymaftools.core.PairwiseMatrix) parse_gene_info() (in module pymaftools.utils.geneinfo) parse_info() (in module pymaftools.io.vcf.parsers) parse_tcga_barcode() (in module pymaftools.io.tcga) parse_vcf_rows() (in module pymaftools.io.vcf.parsers) PCA() (pymaftools.core.PivotTable.PivotTable method) PCA_CCA (class in pymaftools.utils.reduction) PivotStatsPlot (class in pymaftools.plot.PivotStatsPlot) PivotTable (class in pymaftools.core.PivotTable) plot (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable property) (pymaftools.core.ExpressionTable.ExpressionTable property) (pymaftools.core.MAF.MAF property) (pymaftools.core.PivotTable.PivotTable property) (pymaftools.core.SignatureTable.SignatureTable property) plot() (pymaftools.plot.LollipopPlot.LollipopPlot method) plot_all_legends() (pymaftools.plot.BasePlot.BasePlot method) plot_ari_matrix() (in module pymaftools.core.Clustering) plot_bar() (pymaftools.plot.OncoPlot.OncoPlot method) plot_boxplot_with_annot() (pymaftools.plot.PivotStatsPlot.PivotStatsPlot method) plot_categorical_metadata() (pymaftools.plot.OncoPlot.OncoPlot method) plot_cluster_feature_importance() (in module pymaftools.core.Clustering) plot_cluster_feature_importance_boxplot() (in module pymaftools.core.Clustering) plot_clustering_metrics_and_find_best_k() (in module pymaftools.core.Clustering) plot_cnv_band_ratio() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable method) plot_cohort_demo() (pymaftools.plot.MethodsPlot.MethodsPlot method) plot_feature_importance_distribution() (pymaftools.plot.ModelPlot.ModelPlot method) plot_final_coefficients() (pymaftools.model.StackingModel.OmicsStackingModel method) plot_freq() (pymaftools.plot.OncoPlot.OncoPlot method) plot_group_heatmap() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) plot_heatmap() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) plot_horizontal_legend() (pymaftools.plot.LegendManager.LegendManager method) plot_legends() (pymaftools.plot.LegendManager.LegendManager method) plot_metric_comparison_with_annotation() (in module pymaftools.model.modelUtils) (pymaftools.plot.ModelPlot.ModelPlot method) plot_multi_cohort() (pymaftools.plot.LollipopPlot.LollipopPlot class method) plot_numeric_metadata() (pymaftools.plot.OncoPlot.OncoPlot method) plot_pca_legends() (pymaftools.plot.LegendManager.LegendManager method) plot_pca_samples() (pymaftools.plot.PivotStatsPlot.PivotStatsPlot method) plot_permutation_distribution() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) plot_rfecv_curve() (pymaftools.plot.ModelPlot.ModelPlot method) plot_similarity() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) plot_similarity_matrix() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) plot_top_feature_importance_heatmap() (in module pymaftools.model.modelUtils) (pymaftools.plot.ModelPlot.ModelPlot method) pos (pymaftools.io.vcf.record.VCFRecord attribute) predefined_cmaps (pymaftools.plot.ColorManager.ColorManager attribute) predict() (pymaftools.model.StackingModel.OmicsStackingModel method) predict_proba() (pymaftools.model.StackingModel.OmicsStackingModel method) prepare_data() (pymaftools.core.PivotTable.PivotTable static method) prepare_features() (pymaftools.model.StackingModel.OmicsStackingModel method) pyclone_to_sorted_table() (pymaftools.core.CancerCellFractionTable.CancerCellFractionTable static method) pymaftools.core.CancerCellFractionTable module pymaftools.core.Clustering module pymaftools.core.Cohort module

pymaftools.core.CopyNumberVariationTable module pymaftools.core.ExpressionTable module pymaftools.core.MAF module pymaftools.core.PairwiseMatrix module pymaftools.core.PivotTable module pymaftools.core.SignatureTable module pymaftools.core.VCF module pymaftools.io.tcga module pymaftools.io.vcf.parsers module pymaftools.io.vcf.record module pymaftools.model.modelUtils module pymaftools.model.StackingModel module pymaftools.plot.BasePlot module pymaftools.plot.ColorManager module pymaftools.plot.CopyNumberVariationTablePlot module pymaftools.plot.ExpressionTablePlot module pymaftools.plot.FontManager module pymaftools.plot.LegendManager module pymaftools.plot.LollipopPlot module pymaftools.plot.MethodsPlot module pymaftools.plot.ModelPlot module pymaftools.plot.OncoPlot module pymaftools.plot.PivotStatsPlot module pymaftools.plot.SignatureTablePlot module pymaftools.plot.SmallVariationTablePlot module pymaftools.plot.Track module pymaftools.utils.geneinfo module pymaftools.utils.geneset module pymaftools.utils.reduction module

R

read_all_gistic() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable static method) read_and_merge() (pymaftools.io.tcga.TCGACNVGeneBuilder method) (pymaftools.io.tcga.TCGACNVSegmentBuilder method) (pymaftools.io.tcga.TCGAExpressionBuilder method) (pymaftools.io.tcga.TCGAMethylationBuilder method) (pymaftools.io.tcga.TCGAMutationBuilder method) (pymaftools.io.tcga.TCGATableBuilder method) read_cnv_files() (in module pymaftools.core.CopyNumberVariationTable) read_csv() (pymaftools.core.MAF.MAF class method) read_gistic_arm_level() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable class method) read_gistic_gene_level() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable class method) read_GMT() (in module pymaftools.utils.geneset) read_h5() (pymaftools.core.PivotTable.PivotTable class method) read_hdf5() (pymaftools.core.Cohort.Cohort class method) read_maf() (pymaftools.core.MAF.MAF class method) read_sample_cutoff_file() (in module pymaftools.core.CopyNumberVariationTable) read_signature() (pymaftools.core.SignatureTable.SignatureTable class method) read_sqlite() (pymaftools.core.Cohort.Cohort class method) (pymaftools.core.PivotTable.PivotTable class method) read_TCGA_ASCAT3_CNV_file_sheet() (in module pymaftools.core.CopyNumberVariationTable) read_vcf() (pymaftools.core.VCF.VCF class method) ref (pymaftools.io.vcf.record.VCFRecord attribute)

register_fonts_from_directory() (pymaftools.plot.FontManager.FontManager method) register_local_font() (pymaftools.plot.FontManager.FontManager method) reindex() (pymaftools.core.PivotTable.PivotTable method) remove_legend() (pymaftools.plot.BasePlot.BasePlot method) (pymaftools.plot.LegendManager.LegendManager method) remove_table() (pymaftools.core.Cohort.Cohort method) rename_index_and_columns() (pymaftools.core.PivotTable.PivotTable method) render() (pymaftools.plot.OncoPlot.OncoPlot method) (pymaftools.plot.Track.BarTrack method) (pymaftools.plot.Track.CategoricalTrack method) (pymaftools.plot.Track.FreqTrack method) (pymaftools.plot.Track.MainMatrixTrack method) (pymaftools.plot.Track.NumericMatrixTrack method) (pymaftools.plot.Track.NumericTrack method) (pymaftools.plot.Track.Track method) resolve_files() (in module pymaftools.io.tcga) (pymaftools.io.tcga.TCGACNVGeneBuilder method) (pymaftools.io.tcga.TCGATableBuilder method) run_feature_clustering() (in module pymaftools.core.Clustering) run_model_evaluation() (in module pymaftools.model.modelUtils) run_random_forest_cv() (in module pymaftools.core.Clustering) run_random_forest_multiple_seeds() (in module pymaftools.core.Clustering) run_rfecv_feature_selection() (in module pymaftools.model.modelUtils)

S

sample_metadata (pymaftools.core.PivotTable.PivotTable attribute) sample_type() (in module pymaftools.io.vcf.parsers) save() (pymaftools.plot.BasePlot.BasePlot method) select_files() (pymaftools.io.tcga.TCGATableBuilder method) select_samples() (pymaftools.core.MAF.MAF method) set_axis() (pymaftools.plot.LegendManager.LegendManager method) set_config() (pymaftools.plot.OncoPlot.OncoPlot method) setup_matplotlib_fonts() (pymaftools.plot.FontManager.FontManager method) show() (pymaftools.plot.LollipopPlot.LollipopPlot method) side (pymaftools.plot.Track.BarTrack attribute) (pymaftools.plot.Track.CategoricalTrack attribute) (pymaftools.plot.Track.FreqTrack attribute) (pymaftools.plot.Track.MainMatrixTrack attribute) (pymaftools.plot.Track.NumericMatrixTrack attribute) (pymaftools.plot.Track.NumericTrack attribute) (pymaftools.plot.Track.Track attribute) SignatureTable (class in pymaftools.core.SignatureTable) SignatureTablePlot (class in pymaftools.plot.SignatureTablePlot) SimilarityMatrix (class in pymaftools.core.PairwiseMatrix) simulate_alpha_blend() (pymaftools.plot.ColorManager.ColorManager method)

size (pymaftools.plot.Track.Track attribute) SmallVariationTablePlot (class in pymaftools.plot.SmallVariationTablePlot) soft_score() (pymaftools.model.StackingModel.ASCStackingModel method) somatic_interactions() (pymaftools.plot.PivotStatsPlot.PivotStatsPlot method) somatic_interactions_stats() (pymaftools.plot.PivotStatsPlot.PivotStatsPlot method) sort_by_chrom() (pymaftools.core.MAF.MAF method) sort_by_chromosome() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable method) sort_features() (pymaftools.core.PivotTable.PivotTable method) sort_samples_by_group() (pymaftools.core.PivotTable.PivotTable method) sort_samples_by_mutations() (pymaftools.core.PivotTable.PivotTable method) stacked_bar() (pymaftools.plot.SignatureTablePlot.SignatureTablePlot method) subset() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method) (pymaftools.plot.Track.BarTrack method) (pymaftools.plot.Track.CategoricalTrack method) (pymaftools.plot.Track.FreqTrack method) (pymaftools.plot.Track.MainMatrixTrack method) (pymaftools.plot.Track.NumericMatrixTrack method) (pymaftools.plot.Track.NumericTrack method) (pymaftools.plot.Track.Track method) symbol_to_ensembl() (in module pymaftools.utils.geneinfo)

T

table_to_distance() (in module pymaftools.core.Clustering) tail() (pymaftools.core.PivotTable.PivotTable method) TCGA_sample_type() (in module pymaftools.core.CopyNumberVariationTable) TCGAClinicalBuilder (class in pymaftools.io.tcga) TCGACNVGeneBuilder (class in pymaftools.io.tcga) TCGACNVSegmentBuilder (class in pymaftools.io.tcga) TCGAExpressionBuilder (class in pymaftools.io.tcga) TCGAMethylationBuilder (class in pymaftools.io.tcga) TCGAMutationBuilder (class in pymaftools.io.tcga) TCGATableBuilder (class in pymaftools.io.tcga) TITV_CMAP (pymaftools.plot.ColorManager.ColorManager attribute) tmb_by_functional_group (pymaftools.core.MAF.MAF property) TMB_PREFIX (pymaftools.core.MAF.MAF attribute) to_anndata() (pymaftools.core.PivotTable.PivotTable method) to_base_change_pivot_table() (pymaftools.core.MAF.MAF method) to_binary_table() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable method) (pymaftools.core.PivotTable.PivotTable method) to_cluster_table() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable method) (pymaftools.core.ExpressionTable.ExpressionTable method) to_cnv_table() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable static method) to_cooccur_matrix() (pymaftools.core.PivotTable.PivotTable method) to_csv() (pymaftools.core.MAF.MAF method)

to_edges_dataframe() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) to_file() (pymaftools.core.VCF.VCF method) to_gene_table() (pymaftools.core.MAF.MAF method) to_h5() (pymaftools.core.PivotTable.PivotTable method) to_hdf5() (pymaftools.core.Cohort.Cohort method) to_hierarchical_clustering() (pymaftools.core.PivotTable.PivotTable method) to_importance_table() (in module pymaftools.model.modelUtils) to_MAF() (pymaftools.core.MAF.MAF method) to_maf() (pymaftools.core.MAF.MAF method) to_mutation_table() (pymaftools.core.MAF.MAF method) to_networkx_graph() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) to_pivot_table() (pymaftools.core.MAF.MAF method) to_sigprofiler() (pymaftools.core.MAF.MAF method) to_sql_registry() (pymaftools.core.Cohort.Cohort method) to_sqlite() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method) to_thresholded_cnv() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable method) Track (class in pymaftools.plot.Track) transform() (pymaftools.utils.reduction.PCA_CCA method) tumor_ad (pymaftools.io.vcf.record.VCFRecord attribute) tumor_af (pymaftools.io.vcf.record.VCFRecord attribute) tumor_dp (pymaftools.io.vcf.record.VCFRecord attribute) tumor_ref (pymaftools.io.vcf.record.VCFRecord attribute)

U

update_legend_colors() (pymaftools.plot.LegendManager.LegendManager method)

V

vaild_variant_classfication (pymaftools.core.MAF.MAF attribute) valid_variant_classification (pymaftools.core.MAF.MAF attribute) values (pymaftools.plot.Track.BarTrack property)

VCF (class in pymaftools.core.VCF) VCFRecord (class in pymaftools.io.vcf.record) volcano() (pymaftools.plot.ExpressionTablePlot.ExpressionTablePlot method)

W

WEIGHT_MAP (pymaftools.plot.FontManager.FontManager attribute)

write_maf() (pymaftools.core.MAF.MAF method) write_SigProfilerMatrixGenerator_format() (pymaftools.core.MAF.MAF method)