Man pages for LUMC/DGE_analysis
dgeAnalysis
| addAnnotationsFromTableToSE | Add annotation to the SummerizedExperiment. |
| addSamplesFromTableToSE | Add samples to the SummerizedExperiment. |
| alignment_summary | Prepare data for alignment plot |
| barcode | Prepare data for barcode plot |
| barcode_plot | Create barcode plot with ggplot2 |
| bar_plot | Create bar plot with ggplot2 |
| bias_gc | Prepare data for GC bias plot |
| cnet_data | Prepare data for concept network plot |
| cnetPlotly | Genes are gathered from enrichment result from specific... |
| complexity | Prepare data for complexity plot |
| complexityData | Creates dataframe with number of reads per gene, ordered on... |
| count_dist | Prepare data for count distribution plot |
| createContrast | Create contrast by finding matrix values in the design... |
| createDesign | Create vector from two design values and two matrix values.... |
| createMatrix | Getbase column and use this to create right matrix. Loop... |
| dendro_data | Prepare data for dendrogram plot |
| dendro_plot | Create dendrogram plot with ggplot2 |
| de_ratio | Prepare data for expression ratio plot |
| enrich_bar | Prepare data for enriched bar plot |
| enrich_barDE | Prepare data for enriched bar plot with DE genes |
| extract_geneSets | Collect genes within a pathway. Gets genes from enrichment... |
| fix_violin_hover | Fix hover info for violin plot, as it cant find CPM values |
| gene_strand | Prepare data for gene strand bias plot |
| getCount | Count the read counts per feature to find number of reads... |
| get_dendrogram_data | Get heigth information from tree object. Get labels/names... |
| get_organismID | The gene IDs are gathered from DE table. The first part of... |
| heat_de | Prepare data for heatmap plot |
| heatmap_plot | Create heatmap plot with ggplot2 |
| heat_var | Prepare data for heatmap plot |
| informationBox | Template for plot information. |
| line_plot | Create line plot with ggplot2 |
| list2df | The inputList is converted to a dataframe format. Dataframe... |
| list2graph | The inputList is converted to a dataframe. The dataframe is... |
| ma | Prepare data for MA plot |
| mds_clust | Prepare data for MDS plot |
| network_plot | Create network plot with ggplot2 |
| pca_data | Prepare data for PCA plot |
| pvalue_data | Prepare data for pvalue plot |
| readCountsFromTable | Add all counts that are in samples in SummerizedExperiment. |
| relevelSamples | Create vector from two matrix values. Try to relevel samples... |
| scatter_plot | Create scatter plot with ggplot2 |
| stackDge | Stacks total DGE counts based on: mapping feature (aligned,... |
| startApp | Start dgeAnalysis application. |
| tsne_data | Prepare data for tSNE plot |
| violin_dist | Prepare data for violin distribution plot |
| violin_plot | Create violin plot with ggplot2 |
| volcano | Prepare data for volcano plot |
| voom_data | Prepare data for voom plot |
