options(stringsAsFactors = F)

expdata0 = read.table("~/data_RNA_Seq_v2_mRNA.txt",header=T,sep="\t")
View(head(expdata0))


isthereNA <- function(x){
  return(any(is.na(x)))
}
index = apply(expdata0,1,isthereNA)
expdata1 = expdata0[!index,]
View(head(expdata1))      

expdata2 = expdata1[,c(-1,-2)]
rownames(expdata2) = expdata1[,1]
View(head(expdata2))



gene.wanted = 'EFGL2'
gene.wanted.exp = unlist(expdata2[rownames(expdata2) == gene.wanted,])
names(gene.wanted.exp) = NULL

## get correlations with wanted gene
getCorrelationPvalue1 <- function(x){
  pvalue = cor.test(x,gene.wanted.exp,method = "spearman")$p.value
  return(pvalue)
}
getCorrelationPvalue2 <- function(x){
  pvalue = cor.test(x,gene.wanted.exp,method = "pearson")$p.value
  return(pvalue)
}
getCorrelationValue1 <- function(x){
  cor.value = cor.test(x,gene.wanted.exp,method = "spearman")$estimate
  return(cor.value)
}
getCorrelationValue2 <- function(x){
  cor.value = cor.test(x,gene.wanted.exp,method = "pearson")$estimate
  return(cor.value)
}
p.value.spearman = apply(expdata2,1,getCorrelationPvalue1)
p.value.pearson = apply(expdata2,1,getCorrelationPvalue2)
cor.value.spearman = apply(expdata2,1,getCorrelationValue1)
cor.value.pearson = apply(expdata2,1,getCorrelationValue2)

result = data.frame(GeneName = names(p.value.spearman),
                    P.value.Spearman = unlist(p.value.spearman),
                    Cor.value.Spearman = unlist(cor.value.spearman),
                    P.value.Pearson = unlist(p.value.pearson),
                    cor.value.pearson = unlist(cor.value.pearson))
result = result[order(abs(result$Cor.value.Spearman),decreasing = T),]
View(head(result))
write.table(result,"Coexpression_result.txt",col.names = T,row.names = F,quote=F,sep="\t")