combine_enrichmentTests: Run enrichment tests and combine into list

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Description

Run enrichment tests and combine into list

Usage

combine_enrichmentTests(
  diff,
  enrichment_qval,
  qval.th,
  cdiff.th,
  annotFeat_long,
  peak_distance,
  refined_annotation,
  GeneSets,
  GeneSetsDf,
  GenePool
)

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

Value

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

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.