combine_enrichmentTests {ChromSCape} | R Documentation |
Run enrichment tests and combine into list
combine_enrichmentTests( diff, enrichment_qval, qval.th, cdiff.th, annotFeat_long, peak_distance, refined_annotation, GeneSets, GeneSetsDf, GenePool )
diff |
Differential list |
enrichment_qval |
Adusted p-value threshold above which a pathway is considered significative list |
qval.th |
Differential analysis adjusted p.value threshold |
cdiff.th |
Differential analysis log-fold change threshold |
annotFeat_long |
Long annotation |
peak_distance |
Maximum gene to peak distance |
refined_annotation |
Refined annotation data.frame if peak calling is done |
GeneSets |
List of pathways |
GeneSetsDf |
Data.frame of pathways |
GenePool |
Pool of possible genes for testing |
A list of list of pathway enrichment data.frames for Both / Over / Under and for each cluster