WGCNA

加权基因共表达网络分析 (WGCNA, Weighted correlation network analysis)是用来描述不同样品之间基因关联模式的系统生物学方法，可以用来鉴定高度协同变化的基因集,

image.png

测试数据下载地址：https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-Data.zip

source("https://bioconductor.org/biocLite.R")
biocLite(c("AnnotationDbi", "impute","GO.db", "preprocessCore"))
install.packages(c("WGCNA", "stringr", "reshape2"), repos="https://mirrors.tuna.tsinghua.edu.cn/CRAN")
options(stringsAsFactors = FALSE);
#开多线程，但是Mac上似乎这一步会报错，可不做
enableWGCNAThreads()
library(WGCNA);
options(stringsAsFactors = FALSE);

Data input, cleaning and pre-processing

#制作基因表达矩阵
#Read in the female liver data set
femData = read.csv("Documents/project/test/FemaleLiver-Data/LiverFemale3600.csv");
datExpr0 = as.data.frame(t(femData[, -c(1:8)]));
names(datExpr0) = femData$substanceBXH;

###如果基因多的话，可以筛选变化大的基因，减小计算量,也可不做这一步
m.mad <- apply(dataExpr0,1,mad)
dataExpr0 <- dataExpr0[which(m.mad > 
                 max(quantile(m.mad, probs=seq(0, 1, 0.25))[2],0.01)),]

gsg = goodSamplesGenes(datExpr0, verbose = 3);
gsg$allOK

如果有需要去除的样本和基因的话，执行这一步，ok的话跳过这一步

if (!gsg$allOK)
{
  # Optionally, print the gene and sample names that were removed:
  if (sum(!gsg$goodGenes)>0) 
     printFlush(paste("Removing genes:", paste(names(datExpr0)[!gsg$goodGenes], collapse = ", ")));
  if (sum(!gsg$goodSamples)>0) 
     printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples], collapse = ", ")));
  # Remove the offending genes and samples from the data:
  datExpr0 = datExpr0[gsg$goodSamples, gsg$goodGenes]
}

将样本聚类检查是否有离群样本，检测outlier

sampleTree = hclust(dist(datExpr0), method = "average");
plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5, 
     cex.axis = 1.5, cex.main = 2)

这样的样本有outlier,需要cut掉

只留下需要的sample

clust = cutreeStatic(sampleTree, cutHeight = 15, minSize = 10)
table(clust)
# clust 1 contains the samples we want to keep.
keepSamples = (clust==1)
datExpr = datExpr0[keepSamples, ]
nGenes = ncol(datExpr)
nSamples = nrow(datExpr)
sampleTree = hclust(dist(datExpr), method = "average");
plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5, 
     cex.axis = 1.5, cex.main = 2)

image.png

最后完成的基因表达矩阵

制作表达矩阵对应的特征矩阵

traitData = read.csv("Documents/project/test/FemaleLiver-Data/ClinicalTraits.csv");
dim(traitData)
names(traitData)

# remove columns that hold information we do not need.
allTraits = traitData[, -c(31, 16)];
allTraits = allTraits[, c(2, 11:36) ];
# Form a data frame analogous to expression data that will hold the clinical traits.
femaleSamples = rownames(datExpr);
traitRows = match(femaleSamples, allTraits$Mice);
datTraits = allTraits[traitRows, -1];
rownames(datTraits) = allTraits[traitRows, 1];

完成的特征矩阵

image.png

############################################################

2.网络构建和模块检测

2.1Automatic, one-step network construction and module detection

#软阈值筛选##
# Choose a set of soft-thresholding powers
powers = c(c(1:10), seq(from = 12, to=20, by=2))
# Call the network topology analysis function
sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5)
# Plot the results:
sizeGrWindow(9, 5)
par(mfrow = c(1,2));
cex1 = 0.9;
# Scale-free topology fit index as a function of the soft-thresholding power
plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2],
     xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n",
    main = paste("Scale independence"));
text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2],
    labels=powers,cex=cex1,col="red");
# this line corresponds to using an R^2 cut-off of h
abline(h=0.90,col="red")
# Mean connectivity as a function of the soft-thresholding power
plot(sft$fitIndices[,1], sft$fitIndices[,5],
    xlab="Soft Threshold (power)",ylab="Mean Connectivity", type="n",
    main = paste("Mean connectivity"))
text(sft$fitIndices[,1], sft$fitIndices[,5], labels=powers, cex=cex1,col="red")

# 推荐你一个power,这里返回的是6
sft$powerEstimate

参考：
http://blog.genesino.com/2018/04/wgcna/#wgcna%E5%9F%BA%E6%9C%AC%E6%A6%82%E5%BF%B5
https://www.jianshu.com/p/3618f5ff3eb0
https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/