# Integrative Pathway Enrichment Analysis of Multivariate Omics Data

## Documentation for package ‘ActivePathways’ version 2.0.0

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

## Help Pages

ActivePathways | ActivePathways
brownsMethod | Merge p-values using the Brown's method. If scores_direction and constraints_vector parameters are provided this method is called DPM
columnSignificance | Determine which terms are found to be significant using each column individually.
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