performAllNetworkAnalyses: Perform all network-related statistical and descriptive...

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

Perform all network-related statistical and descriptive analyses, including community and enrichment analyses.

Description

A convenience function that calls all network-related functions in one-go, using selected default parameters and a set of adjustable ones also. For full adjustment, run the individual functions separately.

Usage

performAllNetworkAnalyses(
  GRN,
  ontology = c("GO_BP", "GO_MF"),
  algorithm = "weight01",
  statistic = "fisher",
  background = "neighborhood",
  clustering = "louvain",
  communities = seq_len(10),
  display = "byRank",
  topnGenes = 20,
  topnTFs = 20,
  display_pAdj = FALSE,
  outputFolder = NULL,
  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)
clustering	Character. Default louvain. One of: louvain, leiden, leading_eigen, fast_greedy, optimal, walktrap. The community detection algorithm to be used. Please bear in mind the robustness and time consumption of the algorithms when opting for an alternative to the default.
communities	Numeric vector. Default seq_len(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 results for the first and fourth largest communities will be plotted. if display = "byLabel", the results for the communities labeled "1", and "4" will be plotted. If set to NULL, all communities will be plotted
display	Character. Default "byRank". One of: "byRank", "byLabel". Specify whether the communities will by displayed 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.
topnGenes	Integer. Default 20. Number of genes to plot, sorted by their rank or label.
topnTFs	Integer. Default 20. Number of TFs to plot, sorted by their rank or label.
display_pAdj	TRUE or FALSE. Default FALSE. Is the p-value being displayed in the plots the adjusted p-value? This parameter is relevant for KEGG, Disease Ontology, and Reactome enrichments, and does not affect GO enrichments.
outputFolder	Character or NULL. Default NULL. If set to NULL, the default output folder as specified when initiating the object in link{initializeGRN} will be used. Otherwise, all output from this function will be put into the specified folder. We recommend specifying an absolute path.
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 added data from this function.

Examples

# See the Workflow vignette on the GRaNIE website for examples
# GRN = loadExampleObject()
# GRN = performAllNetworkAnalyses(GRN, outputFolder = ".", forceRerun = FALSE)

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