Update

data/Decoder_replica2.txt

@@ -3,5 +3,10 @@ UPN05.TAZ	TAZ	Low	UPN05
 UPN05.CTRL	CTRL	Low	UPN05
 X0826.TAZ	TAZ	Low	UPN03
 X0826.CTRL	CTRL	Low	UPN03
+<<<<<<< HEAD
+X0784.CTRL	CTRL	High	UPN22
+X0327.CTRL	CTRL	High	UPN10
+=======
+>>>>>>> e6e28c9a835d4b9d9f01b2a2e2afe517143e52b4
 X0175.TAZ	TAZ	Low	UPN04
 X0175.CTRL	CTRL	Low	UPN04

script/RNAseq_Analysis.R

@@ -171,18 +171,10 @@ run_GSEA(frame.to.test, signatures.to.test)
 ### Replica 2
 #Read  gene x counts table
 gene = read.table(file = "data/featureCounts_results_replica2.txt", header = T)
-gene = gene[,-c(2,3,4,5,6)]
-rownames(gene) = gene$Geneid
-gene$Geneid = NULL
-colnames(gene) = gsub("BAM.", "", colnames(gene))
-colnames(gene) = unlist(lapply(colnames(gene), function(x) Reduce(function(x,y) paste(x,y, sep = "."), 
-                                                                  unlist(strsplit(x, "\\."))[c(1,2)])
-))
 
 
 #Read decoder file
 decoder = read.table(file = "data/Decoder_replica2.txt", header = T)
-decoder$Sample = gsub("X", "", decoder$Sample)
 rownames(decoder) = decoder$Sample
 
 #Set same order in gene and decoder
@@ -192,16 +184,9 @@ gene = gene[, rownames(decoder)]
 decoder$Senescent = relevel(factor(decoder$Senescent), ref = "Low")
 decoder$Group = relevel(factor(decoder$Group), ref = "CTRL")
 decoder$Group2 = paste(decoder$Senescent, decoder$Group, sep = "_")
-decoder$Group2 = factor(decoder$Group2, levels =  c("Low_CTRL", "Low_ARA", "Low_TAZ", "High_CTRL", "High_ARA", "High_TAZ"))
+decoder$Group2 = factor(decoder$Group2, levels =  c("Low_CTRL", "Low_TAZ", "High_CTRL"))
 
 
-#Build DESeq2 object
-dds <- DESeqDataSetFromMatrix(countData = gene,
-                              colData = decoder,
-                              design= ~ Senescent + Group + Senescent:Group )
-#Run DESeq2
-dds <- DESeq(dds)
-  
 #Build DESeq2 object
 dds1 <- DESeqDataSetFromMatrix(countData = gene,
                                colData = decoder,
@@ -210,28 +195,8 @@ dds1 <- DESeqDataSetFromMatrix(countData = gene,
 dds1 <- DESeq(dds1)
   
 #Extract results
-res.HighARA.LowARA = as.data.frame(DESeq2::results(dds, name =  "SenescentHigh.GroupARA"))
-res.HighARA.LowARA$Gene = rownames(res.HighARA.LowARA)
-res.HighTAZ.LowTAZ = as.data.frame(DESeq2::results(dds, name =  "SenescentHigh.GroupTAZ"))
-res.HighTAZ.LowTAZ$Gene = rownames(res.HighTAZ.LowTAZ)
-res.LowARA.HighARA = as.data.frame(DESeq2::results(dds, contrast = c(0,0,0,0,-1,0)))
-res.LowARA.HighARA$Gene = rownames(res.LowARA.HighARA)
-res.LowTAZ.HighTAZ = as.data.frame(DESeq2::results(dds, contrast = c(0,0,0,0,0,-1)))
-res.LowTAZ.HighTAZ$Gene = rownames(res.LowTAZ.HighTAZ)
-res.ARA.CTRL = as.data.frame(DESeq2::results(dds, contrast = c("Group", "ARA", "CTRL")))
-res.ARA.CTRL$Gene = rownames(res.ARA.CTRL)
-res.TAZ.CTRL = as.data.frame(DESeq2::results(dds, contrast = c("Group", "TAZ", "CTRL")))
-res.TAZ.CTRL$Gene = rownames(res.TAZ.CTRL)
-res.High.Low = as.data.frame(DESeq2::results(dds, contrast = c("Senescent", "High", "Low")))
-res.High.Low$Gene = rownames(res.High.Low)
-res.LowARA.LowCTRL = as.data.frame(DESeq2::results(dds1, contrast = c("Group2", "Low_ARA", "Low_CTRL")))
-res.LowARA.LowCTRL$Gene = rownames(res.LowARA.LowCTRL)
-res.HighARA.HighCTRL = as.data.frame(DESeq2::results(dds1, contrast = c("Group2", "High_ARA", "High_CTRL")))
-res.HighARA.HighCTRL$Gene = rownames(res.HighARA.HighCTRL)
 res.LowTAZ.LowCTRL = as.data.frame(DESeq2::results(dds1, contrast = c("Group2", "Low_TAZ", "Low_CTRL")))
 res.LowTAZ.LowCTRL$Gene = rownames(res.LowTAZ.LowCTRL)
-res.HighTAZ.HighCTRL = as.data.frame(DESeq2::results(dds1, contrast = c("Group2", "High_TAZ", "High_CTRL")))
-res.HighTAZ.HighCTRL$Gene = rownames(res.HighTAZ.HighCTRL)
 res.HighCTRL.LowCTRL = as.data.frame(DESeq2::results(dds1, contrast = c("Group2", "High_CTRL", "Low_CTRL")))
 res.HighCTRL.LowCTRL$Gene = rownames(res.HighCTRL.LowCTRL)
 
@@ -247,17 +212,7 @@ barplot_gene_expression_lfc(tmp, PRC2, "Low Untreated vs High Untreated")
 ### Run GSEA  
 
 #Create list of dataframes
-frame.to.test = list("HighARA.LowARA" = res.HighARA.LowARA,
-                     "HighTAZ.LowTAZ" = res.HighTAZ.LowTAZ,
-                     "LowARA.HighARA" = res.LowARA.HighARA,
-                     "LowTAZ.HighTAZ" = res.LowTAZ.HighTAZ,
-                     "High.Low" = res.High.Low, 
-                     "ARA.CTRL" = res.ARA.CTRL,
-                     "TAZ.CTRL" = res.TAZ.CTRL, 
-                     "LowARA.LowCTRL" = res.LowARA.LowCTRL,
-                     "LowTAZ.LowCTRL" = res.LowTAZ.LowCTRL,
-                     "HighARA.HighCTRL" = res.HighARA.HighCTRL,
-                     "HighTAZ.HighCTRL" = res.HighTAZ.HighCTRL,
+frame.to.test = list("LowTAZ.LowCTRL" = res.LowTAZ.LowCTRL,
                      "HighCTRL.LowCTRL" = res.HighCTRL.LowCTRL)
 
 #Create list of signatures