TCGA数据库与肿瘤数据分析（参考后整理）

1.INTRODUCTION（介绍）

 

1.数据来源

• GDC Legacy Archive
• GDC Harmonized database

2.barcode

2.Install.packages(包安装)

3.数据下载

我们以胆管癌数据为例进行展示

• 下载表达数据

#数据查询（就像你在页面网站上点来点去）
query <- GDCquery(project = "TCGA-CHOL",
+                   data.category = "Transcriptome Profiling",
+                   data.type = "Gene Expression Quantification",
+                   workflow.type = "STAR - Counts",
+                   legacy = FALSE,
+                   experimental.strategy = 'RNA-Seq')




#数据下载
GDCdownload(query = query)

• 数据整理

#数据准备
dataPrep <- GDCprepare(query = query)

#数据整理
library(SummarizedExperiment)
expdat <- assay(dataPrep)
dim(expat)
head(expdat)


#数据调整
library(stringr)
group_list<-ifelse(str_sub(colnames(expdat),14,15) == "01","tumor","normal")
group_list
coldata<-data.frame(row.names = colnames(expdat),
                    condition=group_list)
coldata

• DESeq2差异分析

#差异表达分析
library(DESeq2)
expdat<-round(expdat,0)
dds<-DESeqDataSetFromMatrix(countData = expdat,
                            colData = coldata,
                            design = ~ condition)
keep<-rowSums(counts(dds))>=10
dds<-dds[keep,]
dds<-DESeq(dds)
res<-results(dds,contrast = c("condition","tumor","normal"))
resOrdered <- res[order(res$pvalue),]
DEG <- as.data.frame(resOrdered)
DEG <- na.omit(DEG)
logFC_cutoff<-with(DEG,mean(abs(log2FoldChange))+2*sd(abs(log2FoldChange)))
logFC_cutoff
DEG$change<-as.factor(ifelse(DEG$pvalue<0.05&abs(DEG$log2FoldChange)>logFC_cutoff,
                             ifelse(DEG$log2FoldChange>logFC_cutoff,"UP","DOWN"),
                             "NOT"))

•  差异表达基因文件输出

#文件会默认储存在你所创建的根目录里，你也可以根据自己的需要进行调整
write.csv(DEG,file = "TCGA_CHOL_DEG.csv")

• 差异表达基因可视化（火山图）

#火山图可视化
library(ggplot2)
this_title <- paste0('Cutoff for logFC is ',round(logFC_cutoff,3),
                     '\nThe number of up gene is ',nrow(DEG[DEG$change =='UP',]) ,
                     '\nThe number of down gene is ',nrow(DEG[DEG$change =='DOWN',]))
ggplot(data=DEG,aes(x=log2FoldChange,y=-log10(pvalue),color=change))+
  geom_point(alpha=0.4,size=1.75)+
  labs(x="log2 fold change")+ ylab("-log10 pvalue")+
  ggtitle(this_title)+theme_bw(base_size = 10)+
  theme(plot.title = element_text(size=15,hjust=0.5))+
  scale_color_manual(values=c('blue','black','red'))

过程参考了一下链接进行整理R语言TCGA分析https://zhuanlan.zhihu.com/p/107714916​​​​​​​