cna_run: Run WGCNA

In BCMSLab/rkip: Gene co-expression analysis of RKIP, autophagy and EMT in prostate cancer

Description

A wrapper to run WGCNA with certain options in a particular order

Usage

cna_run(dat, power)

Arguments

dat	A data.frame of transposed expression matrix
power	An integer power of the adjacency matrix

Value

A list of 9 items:

• adj A matrix, the adjacency matrix result of adjacency

• tom A matrix, the TOM similarity matrix result of TOMsimilarity

• diss A matrix, the dissimilary matrix (1 - tom)

• modules A numeric, the assignment of each column to a module after the cutting

• colors A character, the colors given to each integer in modules, result of labels2colors

• mes A data.frame, the eigengenes item of calling moduleEigengenes

• me_dist A matrix, the distance matrix (1 - mes)

• me_tree An hclust, the hierarchial clustering object of me_dist

• merged colors A character, the final lables after mergeCloseModules

Examples

library(Biobase)
data(sample.ExpressionSet)
dat <- list(data = t(exprs(sample.ExpressionSet)))

cna_run(dat$data, power = 5)

BCMSLab/rkip documentation built on May 17, 2019, 2:14 a.m.