co_methylation_step2: The second step of co-methylation analysis

In Gavin-Yinld/coMethy: Co-methylation analysis to cluster the genomic loci with similar methylation pattern

Description

The second step of the co-methylation analysis, i.e. co-methylation analysis in each kmeans cluster based on WGCNA package.

Usage

co_methylation_step2(data,kmeans_result,softPower_list,plot=FALSE)

Arguments

data	methylation profile of pCSM loci in each sample
kmeans_result	a kmeans object including the data and cluster information
softPower_list	a numeric vector contains 3 soft-thresholding power for WGCNA analysis in each kmeans cluster
plot	Logical; determine whether to produce the figures with methylation level of pCSM loci in each WGCNA cluster

Value

An object of "kmeans" with cluster information.

Examples

#module <- co_methylation_step2(data=meth_data,kmeans_result=kmeans_cluster,softPower_list=c(20,16,16),plot=T)

Gavin-Yinld/coMethy documentation built on Aug. 23, 2019, 11:37 p.m.