combine_enrichmentTests: Run enrichment tests and combine into list

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

Run enrichment tests and combine into list

Description

Run enrichment tests and combine into list

Usage

combine_enrichmentTests(
  diff,
  enrichment_qval,
  qval.th,
  logFC.th,
  min.percent,
  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
logFC.th	Differential analysis log-fold change threshold
min.percent	Minimum fraction of cells having the feature active to consider it as significantly differential. (0.01)
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

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.