get_grn {netOmics} | R Documentation |
Get Gene Regulatory Network (GRN) from a data.frame. Optionally, if the gene are clustered, sub_network are build for each cluster.
get_grn(X, cluster = NULL, method = c("aracne"), type = "gene")
X |
a |
cluster |
(optional) clustering result from
|
method |
network building method, one of c('aracne') |
type |
character added to node metadata |
Methods of GRN reconstruction are as follows: 'aracne': use ARACNe algorithm on Mutual Information (MI) adjency matrix to remove low MI edges in triangles.
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.
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')