Integrative Pathway Enrichment Analysis of Multivariate Omics Data

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Documentation for package ‘ActivePathways’ version 2.0.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

ActivePathways	ActivePathways
brownsMethod	Merge p-values using the Brown's method.
columnSignificance	Determine which terms are found to be significant using each column individually.
DPM	Merge p-values using the DPM method.
export_as_CSV	Export the results from ActivePathways as a comma-separated values (CSV) file.
GMT	Read and Write GMT files
gmt	Read and Write GMT files
hypergeometric	Hypergeometric test
is.GMT	Read and Write GMT files
makeBackground	Make a background list of genes (i.e., the statistical universe) based on all the terms (gene sets, pathways) considered.
merge_p_values	Merge a list or matrix of p-values
orderedHypergeometric	Ordered Hypergeometric Test
prepareCytoscape	Prepare files for building an enrichment map network visualization in Cytoscape
read.GMT	Read and Write GMT files
write.GMT	Read and Write GMT files