get_grn: Gene Regulatory Network

In abodein/netOmics: Multi-Omics (time-course) network-based integration and interpretation

Gene Regulatory Network

Description

Get Gene Regulatory Network (GRN) from a data.frame. Optionally, if the gene are clustered, sub_network are build for each cluster.

Usage

get_grn(X, cluster = NULL, method = c("aracne"), type = "gene")

Arguments

X	a data.frame/matrix with gene expression (genes in columns, samples in rows).
cluster	(optional) clustering result from getCluster
method	network building method, one of c('aracne')
type	character added to node metadata

Details

Methods of GRN reconstruction are as follows: 'aracne': use ARACNe algorithm on Mutual Information (MI) adjency matrix to remove low MI edges in triangles.

Value

An igraph object if no cluster informations are given. Otherwise, it returns a list of igraph object (list.igraph) with a subgraph for each cluster and a global graph with all the genes.

See Also

build.mim, aracne, getCluster

Examples

data(hmp_T2D)
# grn only on gene
cluster.mRNA <- timeOmics::getCluster(hmp_T2D$getCluster.res, 
                                      user.block = 'RNA')
X <- hmp_T2D$raw$RNA
grn.res <- get_grn(X = hmp_T2D$raw$RNA, 
                   cluster = cluster.mRNA, 
                   method = 'aracne')

abodein/netOmics documentation built on Oct. 20, 2024, 9:25 a.m.