Calculates GSEA statistics for a given query gene set
Calculates GSEA statistic valus for all gene sets in 'selectedStats' list.
Collapse list of enriched pathways to independent ones.
Collapse list of enriched pathways to independent ones. Version for ORA hypergeometric test.
Example list of mouse Reactome pathways.
Example vector of gene-level statistics obtained for Th1 polarization.
Wrapper to run methods for preranked gene set enrichment analysis.
Runs label-permuring gene set enrichment analysis.
Runs preranked gene set enrichment analysis.
Runs preranked gene set enrichment analysis.
Runs preranked gene set enrichment analysis for preprocessed input data.
Simple overrepresentation analysis based on hypergeometric test
Returns a list of pathways from a GMT file.
Effeciently converts collection of pathways using AnnotationDbi::mapIds function. Parameters are the sames as for mapIds except for keys, which is assumed to be a list of vectors.
Calculates the expected error for the standard deviation of the P-value logarithm.
Calculates P-values for preprocessed data.
Plots GSEA enrichment plot.
Plots table of enrichment graphs using ggplot and gridExtra.
Returns a list of Reactome pathways for given Entrez gene IDs
Write collection of pathways (list of vectors) to a gmt file