#-------------------------------------------------------------------------------
# Environment Declarations
#-------------------------------------------------------------------------------

rm(list=ls())
options(object.size=Inf)
memory.size(max = TRUE)

#-------------------------------------------------------------------------------
# Function Declarations
#-------------------------------------------------------------------------------

source("http://bioconductor.org/biocLite.R")
biocLite()
install.packages("multtest")
library(multtest)
library(stats)

#-------------------------------------------------------------------------------
# GSE20202
#-------------------------------------------------------------------------------

tatata <- read.table("Coded_Linear_FoldChanges_GSE20202.txt",header=TRUE)
running.results <- NULL
temp1 <- tatata[,1]
temp2 <- tatata[,2]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,2][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,3]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,3][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,4]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,4][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,5]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,5][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
write.table(running.results,"cor_results_GSE20202.txt",sep="\t")

#-------------------------------------------------------------------------------
# Pink
#-------------------------------------------------------------------------------

tatata <- read.table("Coded_Linear_FoldChanges_Pink.txt",header=TRUE)
running.results <- NULL
temp1 <- tatata[,1]
temp2 <- tatata[,2]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,2][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,3]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,3][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,4]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,4][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,5]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,5][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
write.table(running.results,"cor_results_pink.txt",sep="\t")

#-------------------------------------------------------------------------------
# GSE26246
#-------------------------------------------------------------------------------

tatata <- read.table("Coded_Linear_FoldChanges_GSE26246.txt",header=TRUE)
running.results <- NULL
temp1 <- tatata[,1]
temp2 <- tatata[,2]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,2][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,3]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,3][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,4]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,4][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,5]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,5][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
write.table(running.results,"cor_results_GSE26246.txt",sep="\t")

#-------------------------------------------------------------------------------
# GSE25009
#-------------------------------------------------------------------------------

tatata <- read.table("Coded_Linear_FoldChanges_GSE25009.txt",header=TRUE)
running.results <- NULL
temp1 <- tatata[,1]
temp2 <- tatata[,2]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,2][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,3]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,3][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,4]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,4][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,5]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,5][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
write.table(running.results,"cor_results_GSE25009.txt",sep="\t")

#-------------------------------------------------------------------------------
# GSE23802
#-------------------------------------------------------------------------------

tatata <- read.table("Coded_Linear_FoldChanges_GSE23802.txt",header=TRUE)
running.results <- NULL
temp1 <- tatata[,1]
temp2 <- tatata[,2]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,2][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,3]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,3][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,4]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,4][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,5]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,5][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
write.table(running.results,"cor_results_GSE23802.txt",sep="\t")

#-------------------------------------------------------------------------------
# GSE10940
#-------------------------------------------------------------------------------

tatata <- read.table("Coded_Linear_FoldChanges_GSE10940.txt",header=TRUE)
running.results <- NULL
temp1 <- tatata[,1]
temp2 <- tatata[,2]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,2][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,3]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,3][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,4]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,4][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,5]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,5][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
write.table(running.results,"cor_results_GSE10940.txt",sep="\t")

#-------------------------------------------------------------------------------
# GSE9571
#-------------------------------------------------------------------------------

tatata <- read.table("Coded_Linear_FoldChanges_GSE9571.txt",header=TRUE)
running.results <- NULL
temp1 <- tatata[,1]
temp2 <- tatata[,2]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,2][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,3]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,3][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,4]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,4][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
temp1 <- tatata[,1]
temp2 <- tatata[,5]!=0
temp1 <- temp1[temp2]
temp2 <- tatata[,5][temp2]
temp3 <- cor.test(temp1,temp2,method="spearman")
temp33 <- p.adjust(temp3[[3]],method = "BH")
temp4 <- c(temp3[[4]],temp3[[3]],temp33,length(temp2))
running.results <- rbind(running.results,temp4)
write.table(running.results,"cor_results_GSE9571.txt",sep="\t")