Man pages for RVA
RNAseq Visualization Automation
| c2BroadSets | This is data to be included in package |
| calc.cfb | Calculate CFB |
| cal.pathway.scores | calculate pathway scores |
| count_table | This is data to be included in package |
| dlPathwaysDB | DL Pathways DB |
| get.cpm.colors | Get CPM Colors |
| get.cutoff.df | Create ggplot object for number of differntially expressed... |
| get.cutoff.ggplot | Create ggplot object for number of differntially expressed... |
| make.cutoff.plotly | Create plotly object for number of DE genes at different... |
| multiPlot | Multi Plot |
| nullreturn | Null Return |
| plot_cutoff | Check number of DE genes at different cutoff combinations |
| plot_cutoff_single | Create plotly object for number of DE genes at different... |
| plot_gene | Plot gene expression |
| plot_heatmap.cfb | Plot a CFB Heatmap |
| plot_heatmap.cpm | Plot a CPM Heatmap |
| plot_heatmap.expr | Plot Heatmap From Raw CPM |
| plot_pathway | Pathway analysis and visualization |
| plot_qq | Plot qqplot |
| plot_volcano | Plot volcanoplot |
| prettyGraphs | Pretty Graphs |
| produce.cutoff.message | Create a message about fold change and pvalues used to... |
| produce.cutoff.warning | Create a warning about pvalue or FDR minimum value |
| reformat.ensembl | Reformat Ensembl GeneIDs |
| sample_annotation | This is data to be included in package |
| sample_count_cpm | This is data to be included in package |
| Sample_disease_gene_set | This is data to be included in package |
| Sample_summary_statistics_table | This is data to be included in package |
| Sample_summary_statistics_table1 | This is data to be included in package |
| secondCutoffErr | Second Cutoff Error |
| transform.geneid | Transform GeneIDs |
| validate.annot | Validate Annotation Table |
| validate.baseline | Validate Baseline Values |
| validate.col.types | Check Summary Statistics Required Column Types |
| validate.comp.names | Validate Comp Names |
| validate.data | Validate Data Input |
| validate.data.annot | Validate Data in the Context of Annotation |
| validate.FC | Validate Foldchange |
| validate.flag | Validate Flag Value Is Valid |
| validate.geneset | Validate Geneset |
| validate.genes.present | Validate genes present |
| validate.numeric | Validate Numeric Column |
| validate.pathways.db | Validate Pathways DB |
| validate.pvalflag | Validate pval flag |
| validate.pval.range | Validate P-value Range |
| validate.pvals | Validate Pvalues |
| validate.single.table.isnotlist | Validate Single Table is not list |
| validate.stats | Validate Summary Statistics File |
| validate.stats.cols | Check Summary Statistics Required Columns |
| wpA2020 | This is data to be included in package |
