RNAseq Visualization Automation

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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