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


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Documentation for package ‘GRaNIE’ version 1.0.7

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addConnections_peak_gene Add peak-gene connections to a 'GRN' object
addConnections_TF_peak Add TF-peak 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.
addTFBS Add TFBS to a 'GRN' object
add_TF_gene_correlation Add TF-gene correlations to a 'GRN' object. The information is currently stored in 'GRN@connections$TF_genes.filtered'. Note that raw p-values are not adjusted.
AR_classification_wrapper Run the activator-repressor classification for the TFs for a 'GRN' object
build_eGRN_graph Builds a graph out of a set of connections
calculateCommunitiesEnrichment Enrichment analysis for the genes in each community in the filtered 'GRN'
calculateCommunitiesStats Generate graph communities and their summarizing statistics
calculateGeneralEnrichment Run an enrichment analysis for the genes in the filtered 'GRN'
calculateTFEnrichment Calculate TF-based GO enrichment
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
filterData Filter data from a 'GRN' object
filterGRNAndConnectGenes Filter the GRN and integrate peak-gene connections.
generateStatsSummary Generate a summary PDF for the number of connections for a 'GRN' object.
genes Get the number of genes for a 'GRN' object.
getCounts Get counts for the various data defined in a 'GRN' object
getGRNConnections Extract connections from a 'GRN' object
getParameters Retrieve parameters for previously used function calls and general parameters for a 'GRN' object.
getTopNodes Retrieve top Nodes in the filtered 'GRN'
GRaNIE *GRaNIE* (*G*ene *R*egul*a*tory *N*etwork *I*nference including *E*nhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information)
GRN-class Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (*eGRNs*)
importTFData Import externally derived TF Activity data. EXPERIMENTAL.
initializeGRN Initialize a '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.
overlapPeaksAndTFBS Overlap peaks and TFBS for a 'GRN' object
peaks Get the number of peaks for a 'GRN' object.
performAllNetworkAnalyses Perform all network-related statistical and descriptive analyses, including community and enrichment analyses.
plotCommunitiesEnrichment Plot community-based enrichment results
plotCommunitiesStats Plot general structure & connectivity statistics for each community in a filtered 'GRN'
plotDiagnosticPlots_peakGene Plot diagnostic plots for peak-gene connections for a 'GRN' object
plotDiagnosticPlots_TFPeaks Plot diagnostic plots for TF-peak connections for a 'GRN' object
plotGeneralEnrichment Plot the general enrichement results
plotGeneralGraphStats Plot general structure and connectivity statistics for a filtered 'GRN'
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 GRN.