In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

WGCNA series

FastWGCNA

FastWGCNA would do a standard WGCNA for given normalized matrix and design object.

## data prepration
library(lucky)
data("rna.fpkm")
data("rna.design")

## WGCNA with no local check.Select first 3000 genes into WGCNA
wgcna <- FastWGCNA(expr.matrix = rna.fpkm,
                   design = rna.design,
                   log.convert = T,
                   check = F,
                   contrast.col = "N.status",
                   contrast.control = "N0",
                   mad.portion = 3000,
                   maxBlockSize = 5000,
                   cutoff.pval = 0.05,
                   corType = "pearson",
                   hub_cutoffSigGM=0.15,
                   hub_MM = 0.8,
                   hub_WeightedQ = 0.05,
                   report = F,
                   save.path = "WGCNA-test",
                   names = "love")

## explore Module-Trait relationship in uni-/multi-dataset

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.