# RNAseq Visualization Automation

## Documentation for package ‘RVA’ version 0.0.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

c2BroadSets | This is data to be included in package
cal.pathway.scores | calculate pathway scores
calc.cfb | Calculate CFB
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 genes with different FDR and fold change cutoff.
get.cutoff.ggplot | Create ggplot object for number of differntially expressed genes with different FDR and fold change cutoff.
make.cutoff.plotly | Create plotly object for number of DE genes at different cutoff combinations
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 cutoff combinations
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 the plot.
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.genes.present | Validate genes present
validate.geneset | Validate Geneset
validate.numeric | Validate Numeric Column
validate.pathways.db | Validate Pathways DB
validate.pval.range | Validate P-value Range
validate.pvalflag | Validate pval flag
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