R/doWGCNA.R

In yufree/xMSannotator: xMSannotator: R package for network based annotation of metabolomics data.

doWGCNA <- function(data_m, deepsplit = 4, minclustsize = 1, 
    cutheight = 0.05) {
    
    # library(WGCNA)
    # fname<-'/Users/karanuppal/Documents/Emory/JonesLab/Projects/NIST_QSTD_60K/apLCMS_with_xMSanalyzer_merged_data/apLCMS_feature_list_at_p1_U_p2cor0.7_CV100.txt'
    # setwd('/Users/karanuppal/Documents/Emory/JonesLab/Projects/NIST_QSTD_60K/apLCMS_with_xMSanalyzer_merged_data/')
    # dataexprA<-read.table(fname,sep='\t',header=TRUE)
    
    # data_m<-t(dataexprA[,-c(1:9)])
    # feat_inf<-paste(dataexprA[,1],dataexprA[,2],sep='_')
    
    ADJdataOne = adjacency(datExpr = data_m, power = 1)  #, power = beta1)
    dissTOMdataOne = TOMdist(ADJdataOne)
    hierTOMdataOne = hclust(as.dist(dissTOMdataOne), method = "complete")
    par(mfrow = c(1, 1))
    pdf("plot.pdf")
    plot(hierTOMdataOne, labels = F, main = "Dendrogram in MB20,MB50")
    
    
    
    # save(list=ls(),file='hier_analysis.Rda')
    
    # colorhdataOne=cutreeDynamic(hierTOMdataOne,distM=
    # dissTOMdataOne,deepSplit=2, pamRespectsDendro = FALSE)
    
    # m1=mergeCloseModules(data_m,colors=colorhdataOne)
    
    # length(table(m1$colors))
    
    colorhdataOne2 = cutreeDynamic(hierTOMdataOne, distM = dissTOMdataOne, 
        deepSplit = deepsplit, minClusterSize = minclustsize, 
        pamRespectsDendro = FALSE)
    
    m2 = mergeCloseModules(data_m, colors = colorhdataOne2)
    length(table(m2$colors))
    
    return(m2)
    
}