calculateCommunitiesEnrichment: Enrichment analysis for the genes in each community in the...

In chrarnold/GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

Enrichment analysis for the genes in each community in the filtered GRN

Description

After the vertices of the filtered GRN are clustered into communities using calculateCommunitiesStats, this function will run a per-community enrichment analysis.

Usage

calculateCommunitiesEnrichment(
  GRN,
  ontology = c("GO_BP", "GO_MF"),
  algorithm = "weight01",
  statistic = "fisher",
  background = "neighborhood",
  selection = "byRank",
  communities = seq_len(10),
  pAdjustMethod = "BH",
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
ontology	Character vector of ontologies. Default c("GO_BP", "GO_MF"). Valid values are "GO_BP", "GO_MF", "GO_CC", "KEGG", "DO", and "Reactome", referring to GO Biological Process, GO Molecular Function, GO Cellular Component, KEGG, Disease Ontology, and Reactome Pathways.
algorithm	Character. Default "weight01". One of: "classic", "elim", "weight", "weight01", "lea", "parentchild". Only relevant if ontology is GO related (GO_BP, GO_MF, GO_CC), ignored otherwise. Name of the algorithm that handles the GO graph structures. Valid inputs are those supported by the topGO library.
statistic	Character. Default "fisher". One of: "fisher", "ks", "t", "globaltest", "sum", "ks.ties". Statistical test to be used. Only relevant if ontology is GO related (GO_BP, GO_MF, GO_CC), and valid inputs are those supported by the topGO library, ignored otherwise. For the other ontologies the test statistic is always Fisher.
background	Character. Default "neighborhood". One of: "all_annotated", "all_RNA", "neighborhood". Set of genes to be used to construct the background for the enrichment analysis. This can either be all annotated genes in the reference genome (all_annotated), all differentially expressed genes (all_RNA), or all the genes that are within the neighborhood of a peak in the GRN (neighborhood)
selection	Character. Default "byRank". One of: "byRank", "byLabel". Specify whether the communities enrichment will by calculated based on their rank, where the largest community (with most vertices) would have a rank of 1, or by their label. Note that the label is independent of the rank.
communities	Numeric vector. Default c(1:10). Depending on what was specified in the display parameter, this parameter would indicate either the rank or the label of the communities to be plotted. i.e. for communities = c(1,4), if display = "byRank" the GO enrichment for the first and fourth largest communities will be calculated if display = "byLabel", the results for the communities labeled "1", and "4" will be plotted.
pAdjustMethod	Character. Default "BH". One of: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr". This parameter is only relevant for the following ontologies: KEGG, DO, Reactome. For the other ontologies, the algorithm serves as an adjustment.
forceRerun	TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.

Value

The same GRN object, with the enrichment results stored in the stats$Enrichment$byCommunity slot.

See Also

plotCommunitiesEnrichment

plotGeneralEnrichment

calculateGeneralEnrichment

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
GRN = calculateCommunitiesEnrichment(GRN, ontology = c("GO_BP"), forceRerun = FALSE)

chrarnold/GRaNIE documentation built on April 28, 2022, 2:18 a.m.