Man pages for jmw86069/jamses
Jam SummarizedExperiment Stats
| check_sedesign | Check SEDesign object |
| choose_annotation_colnames | Choose interesting annotation colnames from a data.frame |
| contrast2comp | Convert contrast to short-form comp, convert comp to contrast |
| contrast2comp_dev | Convert contrast to short-form comp, convert comp to contrast... |
| contrast_colors_by_group | Define contrast colors by group colors |
| contrast_names_to_sedesign | Convert contrast names to sedesign object |
| contrasts_to_factors | Convert SEDesign contrasts to data.frame of design factors |
| contrasts_to_venn_setlists | Convert contrast names to Venn setlists for visual comparison |
| detect_heatmap_components | Detect ComplexHeatmap Heatmap grid layout components |
| draw_oneway_contrast | Draw one-way contrast using block arrows |
| draw_twoway_contrast | Draw two one-way contrasts using block arrows, showing a... |
| ebayes2dfs | Convert limma eBayes fit to data.frame with annotated hits |
| filter_contrast_names | Filter contrast names |
| fold_to_log2fold | Convert normal signed fold change to log2 fold change |
| format_hits | Format list of hit vectors into summary counts |
| groups_to_sedesign | Create SEDesign from experimental groups |
| handle_na_values | Handle NA values in a numeric matrix |
| heatmap_column_group_labels | Add Heatmap column group labels |
| heatmap_se | Heatmap for SummarizedExperiment data |
| hit_array_to_list | Quick conversion of hit_array to hit_list |
| intercalate | Intercalate two or more vectors |
| list2im_opt | Convert list to incidence matrix |
| log2fold_to_fold | Convert log2 fold change to signed fold change |
| make_block_arrow_polygon | Make block arrow polygon coordinates for line segments |
| make_se_test | Make SummarizedExperiment test data |
| mark_stat_hits | Mark statistical hits by threshold cutoffs |
| matrix_normalize | Normalize a numeric data matrix |
| plot_sedesign | Plot sedesign object contrasts |
| point_handedness | Determine which side one point is to another, given a slope... |
| point_slope_intercept | convert point-slope to axis intercept |
| process_sestats_to_hitim | Process sestats input into a hit incidence matrix |
| run_limma_replicate | Run limma contrasts with optional probe replicates |
| save_sestats | Save SE contrast stats output |
| se_collapse_by_column | Collapse SummarizedExperiment data by column |
| se_collapse_by_row | Collapse SummarizedExperiment data by row |
| se_contrast_stats | Compute contrast statistics on SummarizedExperiment data |
| sedesign_to_factors | Convert SEDesign to data.frame of design factors |
| se_detected_rows | SummarizedExperiment heuristics to define detected rows |
| se_normalize | Normalize SummarizedExperiment data |
| se_rbind | Combine SummarizedExperiment objects by row |
| sestats_to_df | Convert sestats to table summary |
| sestats_to_dfs | Extract stats as data.frame from SEStats results |
| se_to_rowcoldata | Get SE colData and rowData |
| shortest_unique_abbreviation | Find the shortest abbrevation to retain unique values |
| shrinkDataFrame | Shrink data.frame by row groups |
| shrink_df | Shrink data.frame by row groups |
| shrink_matrix | Shrink a numeric matrix by groups of rows |
| sort_samples | Sort biological sample labels for experimental design |
| stack_contrasts | Stack a vector of contrasts into a full string |
| strsplitOrdered | Split the elements of an ordered factor vector |
| sub_split_vector | Sub-split a split vector (Internal) |
| update_function_params | Update function default parameters |
| update_list_elements | Update a subset of list elements |
| validate_sedesign | Validate SEDesign object contents |
| voom_jam | Limma-voom customized for Jam |
