Integrative Pathway Enrichment Analysis of Multivariate Omics Data

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Documentation for package ‘ActivePathways’ version 1.1.1

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ActivePathways ActivePathways
brownsMethod Merge p-values using the Brown's method.
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 Hypergemoetric 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