require(edgeR)
rnaseqMatrix0= read.table("/data/images/proton/DKlab/orsalia2/stringtie/transcript_count_matrix.csv",header=T,sep=",")
#data = read.table("/data/images/proton/run125/www/genes.counts.matrix", header=T, row.names=1, com='')
#col_ordering = c(1,2,6,7)

rnaseqMatrix =rnaseqMatrix0;
#rnaseqMatrix = round(rnaseqMatrix)
rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=2,]
#conditions = factor(c(rep("FAGsA", 2), rep("FAGsB", 2)))
#                       1    2     3       4       5     6     7       8       9     10    11    12       13    14       15    16    17    18    19      20 
#conditions = factor(c("KO2","KO2","KOIFN","KOIFN","Ko0","Ko0","KoIL4","KoIL4","Ko6","Ko6","wt0","wt0IL4","wt0","wt0IL4","wt2","wt2","wt6","wt6","wtIFN","wtIFN"))
conditions = factor(c("KO","KO","KO","KO","KO","KO","KO","KO","KO","KO","wt","wt","wt","wt","wt","wt","wt","wt","wt","wt"))

exp_study = DGEList(counts=rnaseqMatrix, group=conditions)
exp_study = calcNormFactors(exp_study)
exp_study = estimateCommonDisp(exp_study)
exp_study = estimateTagwiseDisp(exp_study)
et = exactTest(exp_study)
tTags = topTags(et,n=NULL,adjust.method = "fdr")
r = rownames(tTags)
c=data[r,col_ordering]
#tab <- topTags(lrt)
#write.table(tTags, file="edgeRtranscripts.csv")

col_ordering = c(11,13,5,6)#0h
rnaseqMatrix =rnaseqMatrix0[,col_ordering];rnaseqMatrix = rnaseqMatrix[(rnaseqMatrix[,1]+rnaseqMatrix[,2]>0)&(rnaseqMatrix[,3]+rnaseqMatrix[,4]>0),];conditions = factor(c("WT","WT","KO","KO"));
exp_study = DGEList(counts=rnaseqMatrix, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study)
tTags = topTags(et,n=NULL,adjust.method = "fdr")
r <- rownames(topTags(et)$table)
c=cpm(exp_study)[r, order(exp_study$samples$group)]
x=cbind(as.data.frame(tTags),c)
summary(de <- decideTestsDGE(et, p=0.05))
#detags <- rownames(exp_study)[as.logical(de)]
#plotSmear(et, de.tags=detags)
#abline(h = c(-1, 1), col = "blue")
write.table(tTags, file="edgeRtranscripts-0h.csv")
write.table(x, file="edgeRtranscriptsExpr-0h.csv")

col_ordering = c(15,16,1,2)#2h
rnaseqMatrix =rnaseqMatrix0[,col_ordering];rnaseqMatrix = rnaseqMatrix[(rnaseqMatrix[,1]+rnaseqMatrix[,2]>0)&(rnaseqMatrix[,3]+rnaseqMatrix[,4]>0),];conditions = factor(c("WT","WT","KO","KO"));
exp_study = DGEList(counts=rnaseqMatrix, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study)
tTags = topTags(et,n=NULL,adjust.method = "fdr")
write.table(tTags, file="edgeRtranscripts-2h.csv")
col_ordering = c(17,18,9,10)#6h
rnaseqMatrix =rnaseqMatrix0[,col_ordering];rnaseqMatrix = rnaseqMatrix[(rnaseqMatrix[,1]+rnaseqMatrix[,2]>0)&(rnaseqMatrix[,3]+rnaseqMatrix[,4]>0),];conditions = factor(c("WT","WT","KO","KO"));
exp_study = DGEList(counts=rnaseqMatrix, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study)
tTags = topTags(et,n=NULL,adjust.method = "fdr")
write.table(tTags, file="edgeRtranscripts-6h.csv")
col_ordering = c(19,20,3,4)#IFN
rnaseqMatrix =rnaseqMatrix0[,col_ordering];rnaseqMatrix = rnaseqMatrix[(rnaseqMatrix[,1]+rnaseqMatrix[,2]>0)&(rnaseqMatrix[,3]+rnaseqMatrix[,4]>0),];conditions = factor(c("WT","WT","KO","KO"));
exp_study = DGEList(counts=rnaseqMatrix, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study)
tTags = topTags(et,n=NULL,adjust.method = "fdr")
write.table(tTags, file="edgeRtranscripts-IFN.csv")
col_ordering = c(12,14,7,8)#IL4
rnaseqMatrix =rnaseqMatrix0[,col_ordering];rnaseqMatrix = rnaseqMatrix[(rnaseqMatrix[,1]+rnaseqMatrix[,2]>0)&(rnaseqMatrix[,3]+rnaseqMatrix[,4]>0),];conditions = factor(c("WT","WT","KO","KO"));
exp_study = DGEList(counts=rnaseqMatrix, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study)
tTags = topTags(et,n=NULL,adjust.method = "fdr")
write.table(tTags, file="edgeRtranscripts-IL4.csv")