add 9/10

Author: jmzeng1314

.DS_Store

@@ -0,0 +1,215 @@
+rm(list=ls())
+library(reshape2)
+library(edgeR)
+library(DESeq2)
+
+setwd("G:/mRNA/DEG")
+a=read.table('hisat2_mm10_htseq.txt',stringsAsFactors = F)
+######################################################################
+#ESCTSA01.geneCounts	Nek1	2790
+#ESCTSA01.geneCounts	Nek10	18
+#ESCTSA01.geneCounts	Nek11	2
+#ESCTSA01.geneCounts	Nek2	4945
+######################################################################
+colnames(a)=c('sample','gene','reads')
+exprSet=dcast(a,gene~sample)
+head(exprSet)
+
+# write.table(exprSet[grep("^__",exprSet$gene),],'hisat2.stats.txt',quote=F,sep='\t')
+# exprSet=exprSet[!grepl("^__",exprSet$gene),] 
+
+geneLists=exprSet[,1]
+exprSet=exprSet[,-1]
+head(exprSet)
+
+rownames(exprSet)=geneLists
+colnames(exprSet)=do.call(rbind,strsplit(colnames(exprSet),'\\.'))[,1]
+
+write.csv(exprSet,'raw_reads_matrix.csv') 
+
+keepGene=rowSums(cpm(exprSet)>0) >=2
+table(keepGene);dim(exprSet)
+dim(exprSet[keepGene,])
+exprSet=exprSet[keepGene,]
+rownames(exprSet)=geneLists[keepGene]
+
+str(exprSet)
+
+group_list=c('control','control','treat_12','treat_12','treat_2','treat_2')
+
+write.csv(exprSet,'filter_reads_matrix.csv' )
+ 
+
+
+######################################################################
+###################      Firstly for DEseq2      #####################
+######################################################################
+if(T){
+  
+  suppressMessages(library(DESeq2)) 
+  (colData <- data.frame(row.names=colnames(exprSet), group_list=group_list) )
+  dds <- DESeqDataSetFromMatrix(countData = exprSet,
+                                colData = colData,
+                                design = ~ group_list)
+  dds <- DESeq(dds)
+  png("qc_dispersions.png", 1000, 1000, pointsize=20)
+  plotDispEsts(dds, main="Dispersion plot")
+  dev.off()
+  
+  
+  rld <- rlogTransformation(dds)
+  exprMatrix_rlog=assay(rld) 
+  write.csv(exprMatrix_rlog,'exprMatrix.rlog.csv' )
+  
+  normalizedCounts1 <- t( t(counts(dds)) / sizeFactors(dds) )
+  # normalizedCounts2 <- counts(dds, normalized=T) # it's the same for the tpm value
+  # we also can try cpm or rpkm from edgeR pacage
+  exprMatrix_rpm=as.data.frame(normalizedCounts1) 
+  head(exprMatrix_rpm)
+  write.csv(exprMatrix_rpm,'exprMatrix.rpm.csv' )
+  
+  png("DEseq_RAWvsNORM.png",height = 800,width = 800)
+  par(cex = 0.7)
+  n.sample=ncol(exprSet)
+  if(n.sample>40) par(cex = 0.5)
+  cols <- rainbow(n.sample*1.2)
+  par(mfrow=c(2,2))
+  boxplot(exprSet, col = cols,main="expression value",las=2)
+  boxplot(exprMatrix_rlog, col = cols,main="expression value",las=2)
+  hist(as.matrix(exprSet))
+  hist(exprMatrix_rlog)
+  dev.off()
+  
+  library(RColorBrewer)
+  (mycols <- brewer.pal(8, "Dark2")[1:length(unique(group_list))])
+  cor(as.matrix(exprSet))
+  # Sample distance heatmap
+  sampleDists <- as.matrix(dist(t(exprMatrix_rlog)))
+  #install.packages("gplots",repos = "http://cran.us.r-project.org")
+  library(gplots)
+  png("qc-heatmap-samples.png", w=1000, h=1000, pointsize=20)
+  heatmap.2(as.matrix(sampleDists), key=F, trace="none",
+            col=colorpanel(100, "black", "white"),
+            ColSideColors=mycols[group_list], RowSideColors=mycols[group_list],
+            margin=c(10, 10), main="Sample Distance Matrix")
+  dev.off()
+  
+  cor(exprMatrix_rlog) 
+  
+  
+  res <- results(dds, contrast=c("group_list","treat_2","control"))
+  resOrdered <- res[order(res$padj),]
+  head(resOrdered)
+  DEG_treat_2=as.data.frame(resOrdered)
+  write.csv(DEG_treat_2,"DEG_treat_2_deseq2.results.csv")
+  
+  res <- results(dds, contrast=c("group_list","treat_12","control"))
+  resOrdered <- res[order(res$padj),]
+  head(resOrdered)
+  DEG_treat_12=as.data.frame(resOrdered)
+  write.csv(DEG_treat_12,"DEG_treat_12_deseq2.results.csv")
+  
+  
+  
+}
+
+######################################################################
+###################      Then  for edgeR        #####################
+######################################################################
+if(T){
+  
+  library(edgeR)
+  d <- DGEList(counts=exprSet,group=factor(group_list))
+  d$samples$lib.size <- colSums(d$counts)
+  d <- calcNormFactors(d)
+  d$samples
+  
+  ## The calcNormFactors function normalizes for RNA composition by finding a set of scaling
+  ## factors for the library sizes that minimize the log-fold changes between the samples for most
+  ## genes. The default method for computing these scale factors uses a trimmed mean of Mvalues
+  ## (TMM) between each pair of samples
+  
+  png('edgeR_MDS.png')
+  plotMDS(d, method="bcv", col=as.numeric(d$samples$group))
+  dev.off()
+  
+  # The glm approach to multiple groups is similar to the classic approach, but permits more general comparisons to be made
+  
+  dge=d
+ 
+  design <- model.matrix(~0+factor(group_list))
+  rownames(design)<-colnames(dge)
+  colnames(design)<-levels(factor(group_list))
+  
+  dge <- estimateGLMCommonDisp(dge,design)
+  dge <- estimateGLMTrendedDisp(dge, design)
+  dge <- estimateGLMTagwiseDisp(dge, design)
+  
+  fit <- glmFit(dge, design)
+  
+  lrt <- glmLRT(fit,  contrast=c(-1,1,0))
+  nrDEG=topTags(lrt, n=nrow(exprSet))
+  nrDEG=as.data.frame(nrDEG)
+  head(nrDEG)
+  write.csv(nrDEG,"DEG_treat_12_edgeR.csv",quote = F)
+  
+  lrt <- glmLRT(fit, contrast=c(-1,0,1) )
+  nrDEG=topTags(lrt, n=nrow(exprSet))
+  nrDEG=as.data.frame(nrDEG)
+  head(nrDEG)
+  write.csv(nrDEG,"DEG_treat_2_edgeR.csv",quote = F)
+  summary(decideTests(lrt))
+  plotMD(lrt)
+  abline(h=c(-1, 1), col="blue")
+}
+
+######################################################################
+###################      Then  for limma/voom        #################
+######################################################################
+
+
+suppressMessages(library(limma))
+design <- model.matrix(~0+factor(group_list))
+colnames(design)=levels(factor(group_list))
+rownames(design)=colnames(exprSet)
+
+dge <- DGEList(counts=exprSet)
+dge <- calcNormFactors(dge)
+logCPM <- cpm(dge, log=TRUE, prior.count=3)
+
+v <- voom(dge,design,plot=TRUE, normalize="quantile")
+fit <- lmFit(v, design)
+
+group_list
+cont.matrix=makeContrasts(contrasts=c('treat_12-control','treat_2-control'),levels = design)
+fit2=contrasts.fit(fit,cont.matrix)
+fit2=eBayes(fit2)
+ 
+tempOutput = topTable(fit2, coef='treat_12-control', n=Inf)
+DEG_treat_12_limma_voom = na.omit(tempOutput)
+write.csv(DEG_treat_12_limma_voom,"DEG_treat_12_limma_voom.csv",quote = F)
+
+tempOutput = topTable(fit2, coef='treat_2-control', n=Inf)
+DEG_treat_2_limma_voom = na.omit(tempOutput)
+write.csv(DEG_treat_2_limma_voom,"DEG_treat_2_limma_voom.csv",quote = F)
+
+
+
+png("limma_voom_RAWvsNORM.png",height = 600,width = 600)
+exprSet_new=v$E
+par(cex = 0.7)
+n.sample=ncol(exprSet)
+if(n.sample>40) par(cex = 0.5)
+cols <- rainbow(n.sample*1.2)
+par(mfrow=c(2,2))
+boxplot(exprSet, col = cols,main="expression value",las=2)
+boxplot(exprSet_new, col = cols,main="expression value",las=2)
+hist(as.matrix(exprSet))
+hist(exprSet_new)
+dev.off()
+
+
+
+
+
+

10-RNA-seq-3-groups/hisat2_mm10_htseq.R

@@ -20,7 +20,9 @@
     We can use this scripts to do enrichment for the organisms which are not support by Bioconductor package
     one of them use the GOstats package to do enrichment ,the other use the function writen by me.
 ##7-enrichment-with-newest-kegg/
-    most of the kegg database are to old , for example:org.Hs.egPATH has 5869 entrez genes and 229 pathways
+    most of the kegg database are too old , for example:
+    
+    org.Hs.egPATH has 5869 entrez genes and 229 pathways
     On Augest 2015, there are 6901 entrez genes and 295 pathways
     And now , there are 299 pathways and 6992 genes.
     Address the sustainable growth of kegg database, it's essential to update it.
@@ -29,3 +31,12 @@
 ##8-DEG
     there will be a detailed instruction in the folder, please go ahead .
     just for differential expression analysis !!!
+
+##9-microarray
+
+
+##10-RNA-seq-3-groups
+	there are three groups for this RNA-seq data.
+	treat_2 vs control ,  treat_12 vs control.
+	Using DEseq2,edgeR,and voom(limma).
+	You can conpare these 3 methods.