Integrative Pathway Enrichment Analysis of Multivariate Omics Data


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Documentation for package ‘ActivePathways’ version 2.0.6

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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.
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_gmt Merge and filter GMT files based on a list of term IDs
merge_p_values Merge a list or matrix of p-values
merge_results Merge results from multiple ActivePathways analyses
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