combine_enrichmentTests {ChromSCape} | R Documentation

## Run enrichment tests and combine into list

### 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,
      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

[Package ChromSCape version 1.2.62 Index]