Generate tabulated module assignments and nodes for input to Cystoscape.

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Description

Generate tabulated module assignments and nodes for input to Cystoscape.

Usage

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tabular_module(V, W, H, outdir)

Arguments

V

Output from mirsynergy.

W

An N by M edge weight matrix containing interaction strength between N mRNA and M miRNA.

H

An N by N edge weight matrix containing the binary interaction among the N mRNA (genes).

outdir

Path to save the nodes and edges files.

Value

nodes

data.frame containing edges in each indexed module. Each edge (row) contain the edge weights, the edge type (MMI or GGI), and which module they belong to.

edges

data.frame containing nodes in each indexed module. Each node (row) contain the node name, type (mRNA/miRNA), and which module they belong to.

Author(s)

Yue Li

Examples

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load(system.file("extdata/toy_modules.RData", package="Mirsynergy"))

tabular_module(V,W,H)