Run enrichment tests and combine into list

Source: R/diff_analysis_gene_set_enrichment.R

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,
  progress = NULL
)

Arguments

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
progress

A shiny Progress instance to display progress bar.

Value

A list of list of pathway enrichment data.frames for Both / Over / Under and for each cluster