Man pages for rdocking/amlpmpsupport
Support Functions for AML PMP RNA-Seq Stratification Manuscript
| add_colour_vector_to_concordance | Add colour vector to concordance data frame |
| apply_eln2015_cyto | Apply ELN2015 stratification based on cytogenetics |
| apply_eln2017_cyto | Apply ELN2017 stratification based on cytogenetics |
| apply_eln2017_rna | Apply ELN2017-RNA stratification |
| apply_expression_signature_reclassification | Update an existing stratification by applying a gene... |
| aps_volcano_plot | Draw Volcano Plot for APS DE Comparison |
| calculate_reference_set_coefficient_of_variation | Calculate reference set coefficient of variation |
| calculate_reference_set_mean_expression | Calculate reference set mean expression |
| connect_to_aml_project_orm | Connect to AML Project ORM Database |
| construct_rna_qc_dataframe | Construct a data frame of RNA-SeQC results |
| construct_sailfish_gene_dataframe | Construct a data frame of Sailfish gene-level results |
| convert_sailfish_df_to_matrix | From a data frame of Sailfish gene-level results, construct... |
| density_plotter | Generate a density-plot of expression of selected genes,... |
| downregulated_genes | Pull down-regulated genes |
| eng_log_breaks | Generate a set of breaks using the 'Engineer's log scale' |
| expression_matrix_to_long_df | Transform expression matrix to long data frame |
| expression_summary | Summarize distribution characteristics for a column of... |
| fit_coxph | Fit a Cox proportional hazards model |
| gather_expression_matrix_to_tidy_df | Convert an expression matrix to a tidy DF |
| get_cluster_assignments_for_k | Retrieve cluster assignments for a given value of k |
| ggsave_pdf_and_png | Save ggplot to PDF and PNG |
| grid_arrange_shared_legend | Generate a grid of plots with a shared legend |
| group_tally_table | Group / Tally / Table |
| hit_plotter | Generate a dot-plot of expression of selected genes, facetted... |
| limma_logFC_to_signed_foldchange | Convert limma's logFC value to signed fold-change |
| log2_plus1_transform | Transform data by taking the log2(count+1) |
| long_df_to_ranked_matrix | Transform long data frame to sorted matrix |
| matrix_glimpse | # Report basic information about a matrix |
| munge_voom_to_ipa | Munge differential expression hits in voom format to... |
| nest_libraries_by_patient | Add nested library information to a patient-level data frame |
| num_to_text | Convert a small number to a text representation |
| parse_pavfinder_0.2.0 | Parse PAVfinder 0.2.0 output |
| parse_pavfinder_0.3.0 | Parse PAVfinder 0.3.0 output |
| pathway_enrichment_plot | Generate a plot of enriched pathways |
| pipe | Pipe operator |
| plot_heatmap_for_k | Plot a pheatmap for a single value of k |
| plot_rf_predictions | Plot predictions from a randomForest model |
| plot_survival | Plot survival curves |
| plot_vars_by_coverage | This function takes the long and wide data frames, and plots... |
| plot_vars_by_vaf | Join to the plotting frame and re-plot for VAF |
| pretty_kable | Set a function for pretty-printing kables |
| pretty_num | Set a function for pretty-printing numbers in the text |
| pull_enrichr_enriched_terms | Pull EnrichR enriched terms for a single pathway source |
| pull_enrichr_terms_to_plot | Identify enriched terms across cohorts |
| random_forest_summary | From a random forest model generated by caret, generate... |
| read_filled_variant_tsv | This function reads in the 'long' TSV variant sheets... |
| rescale_genes_by_reference | Rescale all genes by reference expression levels |
| retrieve_db_comments | Retrieve DB Comments |
| retrieve_db_curated_results | Retrieve DB Curated Results |
| retrieve_db_libraries | Retrieve DB Libraries |
| retrieve_db_paths | Retrieve DB Paths |
| retrieve_db_specimens | Retrieve DB Specimens |
| rf_predictions | Extract predictions from a random forest model |
| rna_seqc_parser | Parse output from RNA-SeQC v1.1.8 |
| run_cna_workflow | Run the CNA workflow |
| run_gage_for_feature | Run GAGE gene-set enrichment analysis for a given feature |
| run_voom_for_feature | Run voom for a given feature comparison |
| sailfish_gene_parser_post_0.7.0 | Parse gene-level output from Sailfish >=0.7.0 |
| sailfish_isoform_parser_post_0.7.0 | Parse isoform-level output from Sailfish >=0.7.0 |
| sailfish_isoform_parser_pre_0.7.0 | Parse isoform-level output from Sailfish <0.7.0 |
| scale_by_rolling_mean | Scale expression estimates by rolling mean |
| select_by_position | Quick function for mapping to select out list items |
| split_gatk_format_vals | Split a FORMAT string from GATK-haplotype to get simpler... |
| spread_expression_df_to_matrix | Convert a 'tidy' expression DF to a matrix |
| spread_filled_snv_df_to_wide | This function takes the 'long, filled' data frames with... |
| subset_genes_by_thresholds | Subset expression matrix by thresholds |
| subset_genes_for_plots | Subset the TPM matrix to the genes of interest |
| subset_heatmap | Generate a heatmap for a subset of genes |
| subset_pc_plot | Generate a prinicple component plot for a subset of genes,... |
| subtype_to_disease | From a subtype indication, return a simplified disease type |
| tfl_split_sort | A function to sort TFL IDs into ascending order |
| train_caret_rf | Train a random forest model with caret |
| upregulated_genes | Pull up-regulated genes |
| volcano_plotter | Generate a volcano plot of expression hits |
