Function reference • GRaNIE

All functions
`AR_classification_wrapper()`	Run the activator-repressor classification for the TFs for a `GRN` object
`GRN-class`	Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (eGRNs)
`GRaNIE`	GRaNIE (Gene Regulatory Network Inference including Enhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information)
`addConnections_TF_peak()`	Add TF-peak connections to a `GRN` object
`addConnections_peak_gene()`	Add peak-gene connections to a `GRN` object
`addData()`	Add data to a `GRN` object.
`addData_TFActivity()`	Add TF activity data to GRN object using a simplified procedure for estimating it. EXPERIMENTAL.
`addSNPData()`	Add SNP data to a `GRN` object and associate SNPs to peaks.
`addTFBS()`	Add TFBS to a `GRN` object.
`add_TF_gene_correlation()`	Add TF-gene correlations to a `GRN` object.
`add_featureVariation()`	Quantify and interpret multiple sources of biological and technical variation for features (TFs, peaks, and genes) in a `GRN` object
`build_eGRN_graph()`	Builds a graph out of a set of connections
`calculateCommunitiesEnrichment()`	Run an enrichment analysis for the genes in each community in the filtered `GRN` object
`calculateCommunitiesStats()`	Generate graph communities and their summarizing statistics
`calculateGeneralEnrichment()`	Run an enrichment analysis for the genes in the whole network in the filtered `GRN` object
`calculateTFEnrichment()`	Run an enrichment analysis for the set of genes connected to a particular TF or sets of TFs in the filtered `GRN` object
`changeOutputDirectory()`	Change the output directory of a GRN object
`deleteIntermediateData()`	Optional convenience function to delete intermediate data from the function `AR_classification_wrapper` and summary statistics that may occupy a lot of space
`filterConnectionsForPlotting()`	Filter connections for subsequent visualization with `visualizeGRN()` from the filtered eGRN
`filterData()`	Filter RNA-seq and/or peak data from a `GRN` object
`filterGRNAndConnectGenes()`	Filter TF-peaks and peak-gene connections and combine them to TF-peak-gene connections to construct an eGRN.
`generateStatsSummary()`	Generate a summary for the number of connections for different filtering criteria for a `GRN` object.
`getCounts()`	Get counts for the various data defined in a `GRN` object
`getGRNConnections()`	Extract connections or links from a `GRN` object as a data frame.
`getGRNSummary()`	Summarize a `GRN` object to a named list for comparison with other `GRN` objects.
`getParameters()`	Retrieve parameters for previously used function calls and general parameters for a `GRN` object.
`getTopNodes()`	Retrieve the top nodes (TFs or genes) with respect to either degree or Eigenvector centrality in the filtered `GRN` object.
`importTFData()`	Import externally derived TF Activity data. EXPERIMENTAL.
`initializeGRN()`	Create and initialize an empty `GRN` object.
`loadExampleObject()`	Load example GRN dataset
`nGenes()`	Get the number of genes for a `GRN` object.
`nPeaks()`	Get the number of peaks for a `GRN` object.
`nTFs()`	Get the number of TFs for a `GRN` object.
`overlapPeaksAndTFBS()`	Overlap peaks and TFBS for a `GRN` object
`performAllNetworkAnalyses()`	Perform all network-related statistical and descriptive analyses, including community and enrichment analyses. See the functions it executes in the @seealso section below.
`plotCommunitiesEnrichment()`	Plot community-based enrichment results for a filtered `GRN` object
`plotCommunitiesStats()`	Plot general structure & connectivity statistics for each community in a filtered `GRN`
`plotCorrelations()`	Plot scatter plots of the underlying count data for either TF-peak, peak-gene or TF-gene pairs for a `GRN` object
`plotDiagnosticPlots_TFPeaks()`	Plot diagnostic plots for TF-peak connections for a `GRN` object
`plotDiagnosticPlots_TFPeaks_GC()`	Plot GC-specific diagnostic plots for TF-peak connections for a `GRN` object
`plotDiagnosticPlots_peakGene()`	Plot diagnostic plots for peak-gene connections for a `GRN` object
`plotGeneralEnrichment()`	Plot the general enrichement results
`plotGeneralGraphStats()`	Plot general structure and connectivity statistics for a filtered `GRN` object
`plotPCA_all()`	Produce a PCA plot of the data from a `GRN` object
`plotTFEnrichment()`	Plot TF-based GO enrichment results
`plot_stats_connectionSummary()`	Plot various network connectivity summaries for a `GRN` object
`visualizeGRN()`	Visualize a filtered eGRN in a flexible manner.

Reference

All functions