build_coexp_GEOID {EGAD}R Documentation

Builds a coexpression network given a GEO ID

Description

The function generates a dense coexpression network from expression data stored in GEO. The expression data is downloaded from GEO. Correlation coefficicents are used as to weight the edges of the nodes (genes). Calls get_expression_matrix_from_GEO and build_coexp_network.

Usage

build_coexp_GEOID(gseid, gene.list, method = "spearman", flag = "rank")

Arguments

gseid

string GEO ID of expression experiment

gene.list

array of gene labels

method

correlation method to use, default Spearman's rho

flag

string to indicate if the network should be ranked

Value

net Matrix symmetric


[Package EGAD version 1.20.0 Index]