getTopNodes: Retrieve top Nodes in the filtered 'GRN'

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

Retrieve top Nodes in the filtered GRN

Description

Retrieve top Nodes in the filtered GRN

Usage

getTopNodes(GRN, nodeType, rankType, n = 0.1, use_TF_gene_network = TRUE)

Arguments

GRN	Object of class GRN
nodeType	Character. One of: "gene" or "TF". Node type.
rankType	Character. One of: "degree", "EV". This parameter will determine the criterion to be used to identify the "top" nodes. If set to "degree", the function will select top nodes based on the number of connections they have, i.e. based on their degree-centrality. If set to "EV" it will select the top nodes based on their eigenvector-centrality score in the network.
n	Numeric. Default 0.1. If this parameter is passed as a value between (0,1), 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.
use_TF_gene_network	TRUE or FALSE. Default TRUE. Should the TF-gene network be used (TRUE) or the TF-peak-gene network (FALSE)?

Value

A dataframe with the node names and the corresponding scores used to rank them

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
topGenes = getTopNodes(GRN, nodeType = "gene", rankType = "degree", n = 3)
topTFs = getTopNodes(GRN, nodeType = "TF", rankType = "EV", n = 5)

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