Files in nicohuttmann/pOmics

Framework for proteomics data analysis

R/0_RMD_functions.R R/0_code_helpers.R R/0_create_datasets.R R/0_data_attributes.R R/0_data_construction.R R/0_data_handling.R R/0_data_handling_helpers.R R/0_data_processing.R R/0_internal_data_structure.R R/0_project_setup.R R/0_transfer_data_frames.R R/GOannoatoins.R R/TERM2GENE_2_list.R R/TERMS_in_proteins.R R/add_background_variable.R R/add_combined_dataset.R R/add_data.R R/add_database.R R/add_dataset.R R/add_group_columns.R R/add_import.R R/add_info_from_csv.R R/add_observations_data.R R/add_observations_set.R R/add_segment_pvalue.R R/add_variables_data.R R/adjacency.R R/annot_layer_discrete_x.R R/annotation_data2list.R R/ask_name.R R/assemble_heatmap_rowwise.R R/available_variables_data.R R/axis_limit_breaks.R R/bhc.R R/browse_msigdbr.R R/browse_proteins.R R/build_cor_list.R R/cat_function.R R/change_variables_manually.R R/check_database.R R/choose_taxId.R R/choose_terms.R R/cleanup.R R/cluster_inner_borders.R R/colnames_class.R R/colnames_typeof.R R/common_prefix.R R/compare_enrichment_data.R R/connectivity.R R/copy2global.R R/correct_log2fc_anova.R R/count_variables_per_observation.R R/cutree_.R R/cv.R R/cv_m.R R/data2list.R R/dendrogram.R R/dendrogram2table.R R/distribute_quantiles.R R/distribute_quantiles_inner_limits.R R/do_2w_anova_i.R R/do_GSEA.R R/do_GSEA_KEGG.R R/do_GSEA_MSigDB.R R/do_GSEA_Reactome.R R/do_GSEA_topGO.R R/do_ORA.R R/do_ORA_GO.R R/do_ORA_KEGG.R R/do_ORA_MSigDB.R R/do_ORA_Reactome.R R/do_ORA_TERM2GENE.R R/do_ORA_groups.R R/do_ORA_topGO.R R/do_abundance_summary.R R/do_annotation_composition.R R/do_anova.R R/do_cormat.R R/do_count_id_quant.R R/do_fun_enrich_dend.R R/do_hclust.R R/do_hclust_enrich_T2G.R R/do_hclust_transpose.R R/do_normalize.R R/do_pca.R R/do_reverse_dend.R R/do_scale.R R/do_t.test.R R/do_venn.R R/enrichResult_handling.R R/enrich_dend_.R R/enrich_dend_fisher.R R/enrich_dend_ks.R R/eval_2w_anova_i.R R/eval_anova.R R/eval_dend_enrich.R R/export_info_template.R R/export_pdf.R R/export_tables.R R/extract_mqpar_info.R R/factorize_matrix.R R/findORchoose.R R/find_data_entry.R R/find_data_name.R R/first_element.R R/fisher_test.R R/fun_enrich.R R/fun_enrich_t_test.R R/g2p.R R/geomean.R R/get_GO_proteins.R R/get_GOdata.R R/get_MaxQuant_defaults.R R/get_OrgDb.R R/get_all_variables.R R/get_child_terms.R R/get_cluster_cut.R R/get_cluster_proteins.R R/get_cor_data.R R/get_data_name.R R/get_data_names.R R/get_data_template_names.R R/get_database.R R/get_dataset.R R/get_dataset_attr.R R/get_datasets.R R/get_default_data_name.R R/get_default_dataset.R R/get_defaults.R R/get_info_data.R R/get_input.R R/get_labels_column.R R/get_observations.R R/get_observations_data.R R/get_observations_data_names.R R/get_observations_set.R R/get_observations_sets.R R/get_observations_template.R R/get_protein.R R/get_protein_list.R R/get_proteins_TERM2GENE.R R/get_proteome.R R/get_raw_dataset.R R/get_taxId.R R/get_variables.R R/get_variables_data_names.R R/get_variables_template.R R/gg_extract_legend.R R/gg_legend_position.R R/gg_size.R R/identify_Id_type.R R/identify_data_origin.R R/identify_id_columns.R R/identify_observations.R R/identify_separator.R R/identify_taxId.R R/identify_variables.R R/import_Top100_EV.R R/impute_missForest.R R/in_.R R/intersect_m.R R/is_data_name.R R/is_data_origin.R R/is_dataset.R R/is_info_data.R R/is_observations_data.R R/is_observations_set.R R/is_raw_dataset.R R/is_variables_data.R R/ks_test.R R/last_.R R/latex_abbr_table.R R/list2TERM2GENE.R R/list2group_vector.R R/list_entries2vector.R R/list_files.R R/load_msigdb_data.R R/map_variables.R R/match_v2l.R R/matrix_rows.R R/mean_or_0.R R/merge_TERM2GENE.R R/most_common_character.R R/new_default_data.R R/normalize.R R/nulllist.R R/p2g.R R/p2n.R R/paste_terms_overlap_heatmap.R R/plot_ComplexHeatmap.R R/plot_bar_composition.R R/plot_cormat.R R/plot_count_id_quant.R R/plot_dend_enrich_lines.R R/plot_enrich.R R/plot_enrichment_barplot.R R/plot_euler.R R/plot_gg_bar.R R/plot_gg_bar_anova_eval.R R/plot_gg_box.R R/plot_gg_count_id_quant.R R/plot_gg_heatmap_protein_overlap.R R/plot_gg_heatmap_terms.R R/plot_gg_xy_fc.R R/plot_heatmap.R R/plot_heatmap_.R R/plot_heatmap_discrete.R R/plot_heatmap_discrete_OLD.R R/plot_lines.R R/plot_nothing.R R/plot_pca.R R/plot_upset.R R/plot_venn.R R/plot_volcano.R R/plot_xy.R R/pqn.R R/prep_data.R R/print_code_vector_string.R R/print_options.R R/protein2function.R R/protein2gene.R R/pull_data.R R/remove_dataset.R R/remove_observations_data.R R/remove_variables_data.R R/reorder_data.R R/rm_functions.R R/same_prefix.R R/save2cache.R R/save_results.R R/save_wd.R R/search_dend.R R/select2output.R R/select_DisGeNet.R R/select_UniProt.R R/select_UniProt_2_TERM2GENE.R R/select_fasta.R R/select_org.R R/select_org_2_TERM2GENE.R R/sep_vector2list.R R/set_continuous_axes.R R/set_dataset_attr.R R/set_default_data_name.R R/set_default_dataset.R R/set_default_observations_set.R R/set_diagonal.R R/set_wd.R R/setup_CORUM_annotations.R R/setup_DisGeNet.R R/setup_EV_TOP_100.R R/setup_MSigDB.R R/setup_STRINGdb.R R/setup_UniProt.R R/setup_fun_enrich.R R/setup_org_database.R R/setup_taxonomy_information.R R/significant.R R/similarity.R R/simplify_GO_terms_semantic.R R/simplify_enrichment_results.R R/simplify_set_overlap.R R/str_locate_last.R R/str_rev.R R/strsplit_functions.R R/subset_observations.R R/summary_proteins.R R/summary_proteins_2.R R/t2g.R R/themes.R R/threshold.R R/to_data_.R R/total_proteins_summary.R R/translate_id.R R/useful_UniProt_entries.R R/variables2labels.R R/view_data.R R/which_names.R README.md man/TERM2GENE_2_list.Rd man/TERMS_in_proteins.Rd man/add_background_variable.Rd man/add_combined_dataset.Rd man/add_data.Rd man/add_database.Rd man/add_dataset.Rd man/add_group_columns.Rd man/add_import.Rd man/add_info_from_csv.Rd man/add_observations_data.Rd man/add_observations_set.Rd man/add_raw_dataset.Rd man/add_segment_pvalue.Rd man/add_variables_data.Rd man/adjacency.Rd man/annot_layer_discrete_x.Rd man/annotation_data2list.Rd man/ask_name.Rd man/assemble_heatmap_rowwise.Rd man/available_data_frames.Rd man/available_variables_data.Rd man/axis_limit_breaks.Rd man/bhc.Rd man/browse_msigdbr.Rd man/browse_proteins.Rd man/build_cor_list.Rd man/button_begin.Rd man/button_end.Rd man/cat_function.Rd man/cat_vector_string.Rd man/change_variables_manually.Rd man/check_buttons.Rd man/check_database.Rd man/choose_taxId.Rd man/choose_terms.Rd man/cleanup.Rd man/cluster_inner_borders.Rd man/colnames_class.Rd man/colnames_typeof.Rd man/common_prefix.Rd man/compare_enrichment_data.Rd man/connectivity.Rd man/copy2global.Rd man/copy_template.Rd man/correct_log2fc_anova.Rd man/count_variables_per_observation.Rd man/cutree_.Rd man/cv.Rd man/cv_m.Rd man/data.frame2tibble.Rd man/data2list.Rd man/data2tibble.Rd man/data_input.Rd man/dendrogram.Rd man/dendrogram2table.Rd man/distribute_quantiles.Rd man/distribute_quantiles_inner_limits.Rd man/do_2w_anova_i.Rd man/do_GSEA.Rd man/do_GSEA_KEGG.Rd man/do_GSEA_MSigDB.Rd man/do_GSEA_Reactome.Rd man/do_GSEA_topGO.Rd man/do_ORA.Rd man/do_ORA_GO.Rd man/do_ORA_KEGG.Rd man/do_ORA_MSigDB.Rd man/do_ORA_Reactome.Rd man/do_ORA_TERM2GENE.Rd man/do_ORA_groups.Rd man/do_ORA_topGO.Rd man/do_abundance_summary.Rd man/do_annotation_composition.Rd man/do_anova.Rd man/do_column_summary.Rd man/do_cormat.Rd man/do_count_id_quant.Rd man/do_expr.Rd man/do_fun.Rd man/do_fun_enrich_dend.Rd man/do_hclust.Rd man/do_hclust_enrich_T2G.Rd man/do_hclust_transpose.Rd man/do_normalize.Rd man/do_nothing.Rd man/do_pca.Rd man/do_reverse_dend.Rd man/do_row_summary.Rd man/do_scale.Rd man/do_t.test.Rd man/do_transpose.Rd man/do_venn.Rd man/dot-add_data_attributes.Rd man/dot-data_columns.Rd man/dot-get_data_attributes.Rd man/dot-set_data_attributes.Rd man/dot-template_names.Rd man/dot-transpose_data_attributes.Rd man/dot-update_data_attributes.Rd man/download_template.Rd man/enrichResult2data.frame.Rd man/enrich_dend_.Rd man/enrich_dend_fisher.Rd man/enrich_dend_ks.Rd man/eval_2w_anova_i.Rd man/eval_anova.Rd man/eval_dend_enrich.Rd man/export_DT_fun_enrich.Rd man/export_DT_t.test.Rd man/export_GO_table.Rd man/export_RMD_fun_enrich.Rd man/export_RMD_t.test.Rd man/export_info_template.Rd man/export_pdf.Rd man/export_svg.Rd man/export_tiff.Rd man/extract_mqpar_info.Rd man/factorize_matrix.Rd man/findORchoose.Rd man/find_data_entry.Rd man/first_element.Rd man/fisher_test.Rd man/fun_enrich.Rd man/fun_enrich_t.test.Rd man/g2p.Rd man/geomean.Rd man/get_GO_proteins.Rd man/get_GOdata.Rd man/get_MaxQuant_defaults.Rd man/get_OrgDb.Rd man/get_all_attr.Rd man/get_all_variables.Rd man/get_child_terms.Rd man/get_cluster_cut.Rd man/get_cluster_proteins.Rd man/get_cor_data.Rd man/get_data.Rd man/get_data_name.Rd man/get_data_names.Rd man/get_data_template_names.Rd man/get_database.Rd man/get_dataset.Rd man/get_dataset_attr.Rd man/get_datasets.Rd man/get_default_data_name.Rd man/get_default_dataset.Rd man/get_defaults.Rd man/get_info_data.Rd man/get_input.Rd man/get_labels_column.Rd man/get_obs.Rd man/get_obs_data.Rd man/get_observations.Rd man/get_observations_data.Rd man/get_observations_data_names.Rd man/get_observations_set.Rd man/get_observations_sets.Rd man/get_observations_template.Rd man/get_protein.Rd man/get_protein_list.Rd man/get_proteins_TERM2GENE.Rd man/get_proteome.Rd man/get_raw_dataset.Rd man/get_taxId.Rd man/get_var.Rd man/get_variables.Rd man/get_variables_data.Rd man/get_variables_data_names.Rd man/get_variables_template.Rd man/gg_extract_legend.Rd man/gg_legend.position.Rd man/gg_size.Rd man/identify_data_origin.Rd man/identify_observations.Rd man/identify_separator.Rd man/identify_taxId.Rd man/identify_variables.Rd man/import2grouped_data.Rd man/import2raw_dataset.Rd man/import_Top100_EV.Rd man/import_fasta.Rd man/import_files.Rd man/impute_missForest.Rd man/impute_norm.Rd man/in_.Rd man/include_groups.Rd man/include_observations_data.Rd man/include_variables_data.Rd man/initialize_data_structure.Rd man/intersect_m.Rd man/is_data_name.Rd man/is_data_origin.Rd man/is_dataset.Rd man/is_info_data.Rd man/is_observations_data.Rd man/is_observations_set.Rd man/is_raw_dataset.Rd man/is_variables_data.Rd man/ks_test.Rd man/last_.Rd man/latex_abbr_table.Rd man/list2group_vector.Rd man/list2tibble.Rd man/list_entries2vector.Rd man/list_files.Rd man/load_msigdb_data.Rd man/map_variables.Rd man/map_variables_data.Rd man/match_v2l.Rd man/matrix2tibble.Rd man/matrix_rows.Rd man/mean_or_0.Rd man/merge_TERM2GENE.Rd man/merge_enrichResults.Rd man/most_common_character.Rd man/new_analysis_list.Rd man/new_cache.Rd man/new_databases_list.Rd man/new_dataset.Rd man/new_datasets_list.Rd man/new_default_data.Rd man/new_imports_list.Rd man/new_info_list.Rd man/next_button.Rd man/nice_number.Rd man/normalize.Rd man/nulllist.Rd man/p2g.Rd man/p2n.Rd man/paste_terms_overlap_heatmap.Rd man/plot_ComplexHeatmap.Rd man/plot_bar_composition.Rd man/plot_cormat.Rd man/plot_count_id_quant.Rd man/plot_dend_enrich_lines.Rd man/plot_enrich.Rd man/plot_enrichment_barplot.Rd man/plot_euler.Rd man/plot_gg_bar.Rd man/plot_gg_bar_anova_eval.Rd man/plot_gg_count_id_quant.Rd man/plot_gg_heatmap_protein_overlap.Rd man/plot_gg_heatmap_terms.Rd man/plot_gg_xy_fc.Rd man/plot_heatmap.Rd man/plot_heatmap_discrete.Rd man/plot_lines.Rd man/plot_nothing.Rd man/plot_pca.Rd man/plot_upset.Rd man/plot_venn.Rd man/plot_volcano.Rd man/plot_xy.Rd man/pqn.Rd man/prep_data.Rd man/print_options.Rd man/protein2function.Rd man/protein2gene.Rd man/pull_data.Rd man/put_data.Rd man/quick_protein_count.Rd man/remove_dataset.Rd man/remove_observations_data.Rd man/remove_variables.Rd man/remove_variables_data.Rd man/reorder_data.Rd man/rm_functions.Rd man/same_prefix.Rd man/save2cache.Rd man/save_results.Rd man/save_wd.Rd man/select2output.Rd man/select_DisGeNet.Rd man/select_UniProt.Rd man/select_UniProt_2_TERM2GENE.Rd man/select_fasta.Rd man/select_org.Rd man/select_org_2_TERM2GENE.Rd man/sep_vector2list.Rd man/set_continuous_axes.Rd man/set_dataset_attr.Rd man/set_default_data_name.Rd man/set_default_dataset.Rd man/set_default_observations_set.Rd man/set_diagonal.Rd man/set_wd.Rd man/setup_CORUM_annotations.Rd man/setup_DisGeNET.Rd man/setup_EV_TOP_100.Rd man/setup_STRINGdb.Rd man/setup_UniProt.Rd man/setup_folders.Rd man/setup_fun_enrich.Rd man/setup_msigdb.Rd man/setup_org_database.Rd man/setup_taxonomy_information.Rd man/significant.Rd man/similarity.Rd man/simplify_GO_terms_semantic.Rd man/simplify_enrichment_results.Rd man/simplify_set_overlap.Rd man/str_locate_last.Rd man/str_rev.Rd man/strsplit_.Rd man/strsplit_keep.Rd man/strsplit_keep_first.Rd man/strsplit_keep_firstn.Rd man/subset_observations.Rd man/subset_variables.Rd man/summary_proteins.Rd man/summary_proteins_2.Rd man/t2g_get_genes.Rd man/t2g_get_matrix.Rd man/t2g_get_terms.Rd man/t2g_subset_genes.Rd man/t2g_subset_terms.Rd man/theme_epitope_peptides_plot.Rd man/theme_hjv_framed.Rd man/theme_hjv_framed_no_axes.Rd man/theme_hjv_half_open.Rd man/theme_hjv_heatmap.Rd man/theme_hjv_heatmap_only.Rd man/theme_hjv_heatmap_only_noframe.Rd man/theme_hjv_overlap_heatmap.Rd man/theme_iDC_annot_layer.Rd man/theme_iDC_dendrogram.Rd man/theme_iDC_heatmap_labels_x.Rd man/theme_iDC_heatmap_labels_y.Rd man/theme_iDC_heatmap_w_legend.Rd man/theme_phosprot_half_open.Rd man/theme_thesis_cor_matrix.Rd man/theme_thesis_framed_no_axis.Rd man/threshold.Rd man/tibble2data.frame.Rd man/tibble2matrix.Rd man/to_data_.Rd man/total_proteins_summary.Rd man/transfer_data_frames.Rd man/transfer_observations.Rd man/transfer_variables_data.Rd man/translate_Ids.Rd man/transpose_tibble.Rd man/useful_UniProt_entries.Rd man/v_db.Rd man/v_ds.Rd man/v_imp.Rd man/v_info.Rd man/variables2labels.Rd man/view_data.Rd man/view_default_attr.Rd man/view_observations.Rd man/view_variables.Rd man/which_names.Rd