GDCRNATools：加利福尼亞大學(xué)生物與植物科學(xué)系植物基因組學(xué)中LNCRNA、miRNA和mRNA數(shù)據(jù)的綜合分析軟件包

GDC：基因組數(shù)據(jù)共享

• 數(shù)據(jù)下載
• ceRNA網(wǎng)絡(luò)分析
• 差異表達分析
• 功能富集分析
• 生存分析
• 數(shù)據(jù)可視化 火山圖、熱圖、GO富集分析結(jié)果、KEGG富集分析結(jié)果等

幫助文檔鏈接 http://bioconductor.org/packages/devel/bioc/vignettes/GDCRNATools/inst/doc/GDCRNATools.html

library(GDCRNATools)
project<-'TCGA-CHOL'
rnadir<-paste(project,'RNAseq',sep='/')
mirdir<-paste(project,'miRNAs',sep="/")
gdcRNADownload(project.id = 'TCGA-CHOL',
              data.type = 'RNAseq',
              write.manifest = F,
              method = 'gdc-client',
              directory = rnadir)

在linux系統(tǒng)中重復(fù)到這一步的時候遇到報錯 ImportError: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /tmp/_MEIylVP0W/libstdc++

我的解決辦法是把它默認下載的gdc-client_v1.3.0替換掉，我換成gdc-client_v1.5.0，下載地址是https://gdc.cancer.gov/access-data/gdc-data-transfer-tool

gdcRNADownload(project.id = 'TCGA-CHOL',
              data.type = 'miRNAs',
              write.manifest = F,
              method = 'gdc-client',
              directory = mirdir)
clinicaldir<-paste(project,'Clinical',sep='/')
gdcClinicalDownload(project.id = 'TCGA-CHOL',
                   write.manifest = F,
                   method='gdc-client',
                   directory = clinicaldir)
metaMatrix.RNA<-gdcParseMetadata(project.id = 'TCGA-CHOL',
                                data.type = 'RNAseq',
                                write.meta = F)
metaMatrix.RNA<-gdcFilterDuplicate(metaMatrix.RNA)
metaMatrix.RNA<-gdcFilterSampleType(metaMatrix.RNA)

metaMatrix.MIR<-gdcParseMetadata(project.id = 'TCGA-CHOL',
                                data.type = 'miRNAs',
                                write.meta = F)
metaMatrix.MIR

metaMatrix.MIR<-gdcFilterDuplicate(metaMatrix.MIR)
metaMatrix.MIR<-gdcFilterSampleType(metaMatrix.MIR)

獲取表達矩陣

rnaCounts<-gdcRNAMerge(metadata = metaMatrix.RNA,
                      path = rnadir,
                      organized = FALSE,
                      data.type = 'RNAseq')
mirCounts<-gdcRNAMerge(metadata = metaMatrix.MIR,
                      path = mirdir,
                      organized = FALSE,
rnaCounts[1:5,1:5]
mirCounts[1:5,1:5]

標(biāo)準(zhǔn)化表達數(shù)據(jù)

rnaExpr<-gdcVoomNormalization(counts=rnaCounts,filter=F)
mirExpr<-gdcVoomNormalization(counts=mirCounts,filter=F)
rnaExpr[1:5,1:5]
mirExpr[1:5,1:5]

差異表達分析

DEGAll<-gdcDEAnalysis(counts = rnaCounts,
                     group=metaMatrix.RNA$sample_type,
                     comparison = 'PrimaryTumor-SolidTissueNormal',
                     method='limma')
deALL<-gdcDEReport(deg=DEGAll,gene.type = 'all')
deLNC<-gdcDEReport(deg=DEGAll,gene.type='long_non_coding')
dePC<-gdcDEReport(deg=DEGAll,gene.type = 'protein_coding')

記下來是數(shù)據(jù)可視化展示

gdcBarPlot(deg=deALL,angle = 45,data.type = 'RNAseq')

 

這里TEC和IG分別是啥？

gdcVolcanoPlot(deLNC)

 

degName<-rownames(deLNC)
gdcHeatmap(deg.id = degName,metadata = metaMatrix.RNA,rna.expr = rnaExpr)

 

enrichOutput<-gdcEnrichAnalysis(gene=rownames(deALL),
                               simplify=T)
gdcEnrichPlot(enrichOutput,type='bar',category = 'GO',num.terms = 10)

畫圖的時候遇到報錯 Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : invalid graphics state 不知道原因出在哪里，但是保存到本地沒問題

pdf(file="../goenrich.pdf",width = 15,height = 15)
gdcEnrichPlot(enrichOutput,type='bar',category = 'GO',num.terms = 10)
dev.off()

 

ceOUtput<-gdcCEAnalysis(lnc=rownames(deLNC),
                       pc=rownames(dePC),
                       lnc.targets = 'starBase',
                       pc.targets = 'starBase',
                       rna.expr = rnaExpr,
                       mir.expr = mirExpr)
edges<-gdcExportNetwork(ceNetwork = ceOutput2,net='edges')
nodes<-gdcExportNetwork(ceNetwork = ceOutput2,net='nodes')
write.table(edges,file='edges.txt',sep='\t',quote=F)
write.table(nodes,file="nodes.txt",sep="\t",quote=F)

最后生成了兩個文件，如何用cytoscape可視化這兩個文件我暫時還不知道如何實現(xiàn)。