Amberkar_Scripts/msbb_array_diffcoexp2_TED_TDD_analysis.R at master · hidelab/Amberkar_Scripts · GitHub

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library(diffcoexp)
library(org.Hs.eg.db)
library(dplyr)
library(magrittr)
library(enrichR)
library(data.table)
library(foreach)
library(doParallel)
library(DCGL)

#setwd("/Users/sandeepamberkar/Work/Data/MSMM-MSBB-HBTRC-Data/MSBB_Array19/GSE84422/")
setwd("/shared/hidelab2/user/md4zsa/Work/Data/MSBB_Array19/GSE84422")
msbb_gse84422_GPL96_97_samplesToAnalyse.exprs=readRDS("msbb_gse84422_GPL96_97_samplesToAnalyse_exprs.RDS")
names(msbb_gse84422_GPL96_97_samplesToAnalyse.exprs)=gsub(pattern = " ",replacement = "_",x = names(msbb_gse84422_GPL96_97_samplesToAnalyse.exprs))
msbb_gse84422_GPL570_samplesToAnalyse.exprs=readRDS("msbb_gse84422_GPL570_samplesToAnalyse_exprs.RDS")
names(msbb_gse84422_GPL570_samplesToAnalyse.exprs)=gsub(pattern = " ",replacement = "_",x = names(msbb_gse84422_GPL570_samplesToAnalyse.exprs))
regnet_tf2target.HGNC=fread("/shared/hidelab2/user/md4zsa/Work/Data/TF_Databases/RegNetwork_human_regulators2.txt",header = T,sep = "\t",showProgress = T,data.table = F)%>%dplyr::filter(evidence=="Experimental")%>%dplyr::select(c(regulator_symbol,target_symbol))
#regnet_tf2target.HGNC=fread("/Users/sandeepamberkar/Work/Data/TF_Databases/RegNetwork_human_regulators2.txt",header = T,sep = "\t",showProgress = T,data.table = F)%>%filter(evidence=="Experimental")%>%dplyr::select(c(regulator_symbol,target_symbol))

msbb_gse84422_diffcoexp_results_files=list.files(path = ".",pattern = "diffcoexp")%>%grep(pattern = ".RDS",value = T)%>%sort
msbb_gse84422_diffcoexp_results=vector(mode = "list",length = length(msbb_gse84422_diffcoexp_results_files))
names(msbb_gse84422_diffcoexp_results)=gsub(pattern = " ",unlist(lapply(lapply(msbb_gse84422_diffcoexp_results_files,function(y)strsplit(x = y,split = "_")[[1]]),`[[`,1)),replacement = "_")
for(f in 1:19){
  msbb_gse84422_diffcoexp_results[[f]]=readRDS(msbb_gse84422_diffcoexp_results_files[f])
}
msbb_gse84422.DCGs=lapply(msbb_gse84422_diffcoexp_results,function(x)x$DCGs)
msbb_gse84422.DCGs_list=lapply(msbb_gse84422.DCGs,function(x)x%>%dplyr::filter(q<=0.05)%>%pull(Gene))
msbb_gse84422.DCLs=lapply(msbb_gse84422_diffcoexp_results,function(x)x$DCLs)
msbb_gse84422.DCLs_filtered=lapply(msbb_gse84422_diffcoexp_results,function(x)x$DCLs%>%filter(q.diffcor<=0.05))

mc=8
cl=makeCluster(mc)
msbb_array_DRrank.TDD=msbb_array_DRrank.TED=vector(mode = "list",length = 19)
names(msbb_array_DRrank.TDD)=names(msbb_array_DRrank.TED)=names(msbb_gse84422_diffcoexp_results)
msbb_array_DRrank.TDD[c(1,10)]=mcmapply(FUN=function(a,b)DRrank(DCGs = a,DCLs = b,tf2target = regnet_tf2target.HGNC,expGenes = rownames(msbb_gse84422_GPL570_samplesToAnalyse.exprs$Amygdala),rank.method = "TDD",Nperm = 500),msbb_gse84422.DCGs[c(1,10)],msbb_gse84422.DCLs[c(1,10)],mc.cores = mc)
msbb_array_DRrank.TDD[c(1:9,11:19)]=mcmapply(FUN=function(a,b)DRrank(DCGs = a,DCLs = b,tf2target = regnet_tf2target.HGNC,expGenes = rownames(msbb_gse84422_GPL570_samplesToAnalyse.exprs$Amygdala),rank.method = "TDD",Nperm = 500),msbb_gse84422.DCGs[c(1:9,11:19)],msbb_gse84422.DCLs[c(1:9,11:19)],mc.cores = mc)
msbb_array_DRrank.TED[c(1,10)]=mcmapply(FUN=function(a,b)DRrank(DCGs = a,DCLs = b,tf2target = regnet_tf2target.HGNC,expGenes = rownames(msbb_gse84422_GPL570_samplesToAnalyse.exprs$Amygdala),rank.method = "TED",Nperm = 500),msbb_gse84422.DCGs[c(1,10)],msbb_gse84422.DCLs[c(1,10)],mc.cores = mc)
msbb_array_DRrank.TED[c(1:9,11:19)]=mcmapply(FUN=function(a,b)DRrank(DCGs = a,DCLs = b,tf2target = regnet_tf2target.HGNC,expGenes = rownames(msbb_gse84422_GPL570_samplesToAnalyse.exprs$Amygdala),rank.method = "TED",Nperm = 500),msbb_gse84422.DCGs[c(1:9,11:19)],msbb_gse84422.DCLs[c(1:9,11:19)],mc.cores = mc)