corgraph: Construction of a network graph from correlation matxix

In shkonishi/cornet: Cunstruction of correlation network form transcriptome data

Description

Construction of a correlation network graph from correlation matrix through Random Matrix Theory-based methods. if negetive correlation exists, these information were added to result of igraph object.

Usage

corgraph(mat, thresh = seq(0.30,0.99,by=0.01))

Arguments

mat	correlation matrix
thresh	a vector of threshold sequence as iteration. The initial value as default, 'thresh =seq(0.30,0.99,by=0.01)' if using an arbitral threshold, set a threshold value like as "thresh = 0.85".

Value

A list consists from one igraph object and two dataframes. The one is a weighted edge list, the another one is a result from ks-test of difference eigen sequence based on thresh correlation matrix.

Examples

# # arguments
# nfpkm <- as.data.frame(rskodat::nfpkm)
# res_cld <- cornet::dycutdf(dat = nfpkm, column = -1:-4)$cluster_dat
# cormat <- cor(res_cld[["3"]])
# # create cor graph with a selected cluster
# res <- corgraph(mat = cormat)
# res[[1]]
# head(res[[2]])
# head(res[[3]])

shkonishi/cornet documentation built on May 30, 2019, 7:09 p.m.