calculateTFEnrichment: Calculate TF-based GO enrichment

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

Calculate TF-based GO enrichment

Description

This function calculates the GO enrichment per TF, i.e. for the set of genes a given TF is connected to in the filtered GRN.

Usage

calculateTFEnrichment(
  GRN,
  rankType = "degree",
  n = 3,
  TF.names = NULL,
  ontology = c("GO_BP", "GO_MF"),
  algorithm = "weight01",
  statistic = "fisher",
  background = "neighborhood",
  pAdjustMethod = "BH",
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
rankType	Character. Default "degree". One of: "degree", "EV", "custom". This parameter will determine the criterion to be used to identify the "top" TFs. If set to "degree", the function will select top TFs based on the number of connections to genes they have, i.e. based on their degree-centrality. If set to "EV" it will select the top TFs based on their eigenvector-centrality score in the network. If set to custom, a set of TF names will have to be passed to the "TF.names" parameter.
n	Numeric. Default 3. If this parameter is passed as a value between 0 and 1, it is treated as a percentage of top nodes. If the value is passed as an integer it will be treated as the number of top nodes. This parameter is not relevant if rankType = "custom".
TF.names	Character vector. Default NULL. If the rank type is set to "custom", a vector of TF names for which the GO enrichment should be calculated should be passed to this parameter.
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)
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$Enrichment$byTF slot.

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN =  loadExampleObject()
GRN =  calculateTFEnrichment(GRN, n = 5, ontology = "GO_BP", forceRerun = FALSE)

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