Function reference
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check_sedesign() - Check SEDesign object
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choose_annotation_colnames() - Choose interesting annotation colnames from a data.frame
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contrast2comp()comp2contrast()names_contrast2comp()names_comp2contrast() - Convert contrast to short-form comp, convert comp to contrast
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contrast2comp_dev() - Convert contrast to short-form comp, convert comp to contrast (DEV)
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contrast_colors_by_group() - Define contrast colors by group colors
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contrast_names_to_sedesign() - Convert contrast names to sedesign object
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contrasts_to_factors() - Convert SEDesign contrasts to data.frame of design factors
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contrasts_to_venn_setlists() - Convert contrast names to Venn setlists for visual comparison
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detect_heatmap_components() - Detect ComplexHeatmap Heatmap grid layout components
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draw_oneway_contrast() - Draw one-way contrast using block arrows
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draw_twoway_contrast() - Draw two one-way contrasts using block arrows, showing a two-way connector
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ebayes2dfs() - Convert limma eBayes fit to data.frame with annotated hits
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filter_contrast_names() - Filter contrast names
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fold_to_log2fold() - Convert normal signed fold change to log2 fold change
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format_hits() - Format list of hit vectors into summary counts
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groups_to_sedesign() - Create SEDesign from experimental groups
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handle_na_values() - Handle NA values in a numeric matrix
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heatmap_column_group_labels() - Add Heatmap column group labels
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heatmap_se() - Heatmap for SummarizedExperiment data
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hit_array_to_list() - Quick conversion of hit_array to hit_list
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intercalate() - Intercalate two or more vectors
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list2im_opt() - Convert list to incidence matrix
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log2fold_to_fold() - Convert log2 fold change to signed fold change
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make_block_arrow_polygon() - Make block arrow polygon coordinates for line segments
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make_se_test() - Make SummarizedExperiment test data
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mark_stat_hits() - Mark statistical hits by threshold cutoffs
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matrix_normalize() - Normalize a numeric data matrix
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plot_sedesign() - Plot sedesign object contrasts
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point_handedness() - Determine which side one point is to another, given a slope or angle
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point_slope_intercept() - convert point-slope to axis intercept
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process_sestats_to_hitim() - Process sestats input into a hit incidence matrix
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run_limma_replicate() - Run limma contrasts with optional probe replicates
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save_sestats() - Save SE contrast stats output
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se_collapse_by_column() - Collapse SummarizedExperiment data by column
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se_collapse_by_row() - Collapse SummarizedExperiment data by row
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se_contrast_stats() - Compute contrast statistics on SummarizedExperiment data
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se_detected_rows() - SummarizedExperiment heuristics to define detected rows
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se_normalize() - Normalize SummarizedExperiment data
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se_rbind() - Combine SummarizedExperiment objects by row
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se_to_rowcoldata() - Get SE colData and rowData
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sedesign_to_factors() - Convert SEDesign to data.frame of design factors
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sestats_to_df() - Convert sestats to table summary
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sestats_to_dfs() - Extract stats as data.frame from SEStats results
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shortest_unique_abbreviation() - Find the shortest abbrevation to retain unique values
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shrinkDataFrame() - Shrink data.frame by row groups
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shrink_df() - Shrink data.frame by row groups
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shrink_matrix() - Shrink a numeric matrix by groups of rows
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sort_samples() - Sort biological sample labels for experimental design
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stack_contrasts() - Stack a vector of contrasts into a full string
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strsplitOrdered() - Split the elements of an ordered factor vector
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sub_split_vector() - Sub-split a split vector (Internal)
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update_function_params() - Update function default parameters
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update_list_elements() - Update a subset of list elements
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validate_sedesign() - Validate SEDesign object contents
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voom_jam() - Limma-voom customized for Jam