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 |