activeSignaling: Create gene regulator subnetworks based on gene signature...

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Create gene regulator subnetworks based on gene signature value.

Description

Create subnetworks based on the gene signature value for each node in the summary and for each target in the node.

Usage

activeSignaling(data, sampTab, markers, grn, summary, fc = 5)

Arguments

data	dgCMatrix; gene expression in each cell, found in CellRouter@ndata.
sampTab	data frame; the metadata information of the cells, found in CellRouter@sampTab.
markers	data frame; the gene signatures as calculated by the findSignatures function of CellRouter.
grn	data frame; the gene regulatory network table (GRN_table) as calculated by the buildGRN method of CellRouter.
summary	data frame; the summary of the files obtained in the findpaths.simple function.
fc	numeric; keep only vertex which signature value is smaller than the fold changes.

Value

list; the pathways and the gene regulatory networks (gnrs). The pathways contain the lists of genes that are the markers and the regulators of the target populations for each interaction. The gnrs contain the regultory sub network for each node in the summary and for each target in the node.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.