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library(GDCRNATools)
library(DT)
load RNA counts data
data(rnaCounts)
load miRNAs counts data
data(mirCounts)
####### Normalization of RNAseq data #######
rnaExpr <- gdcVoomNormalization(counts = rnaCounts, filter = FALSE)
####### Normalization of miRNAs data #######
mirExpr <- gdcVoomNormalization(counts = mirCounts, filter = FALSE)
3.1.2 Parse metadata
####### Parse and filter RNAseq metadata #######
metaMatrix.RNA <- gdcParseMetadata(project.id = 'TCGA-CHOL',
data.type = 'RNAseq',
write.meta = FALSE)
metaMatrix.RNA <- gdcFilterDuplicate(metaMatrix.RNA)
metaMatrix.RNA <- gdcFilterSampleType(metaMatrix.RNA)
metaMatrix.RNA[1:5,]
注意comparision寫法順序，誰在前誰是分子，后者是分母
比較對相的來自 metaMatrix.RNA$sample_type函數(shù)的字符串
DEGAll <- gdcDEAnalysis(counts = rnaCounts,
group = metaMatrix.RNA$sample_type,
comparison = 'PrimaryTumor-SolidTissueNormal',
method = 'limma')
DEGAll[1:5,]
All DEGs
deALL <- gdcDEReport(deg = DEGAll, gene.type = 'all')
DE long-noncoding
deLNC <- gdcDEReport(deg = DEGAll, gene.type = 'long_non_coding')
DE protein coding genes
dePC <- gdcDEReport(deg = DEGAll, gene.type = 'protein_coding')
3.2.2 ceRNAs network analysis of DEGs
ceOutput <- gdcCEAnalysis(lnc = rownames(deLNC),
pc = rownames(dePC),
lnc.targets = 'starBase',
pc.targets = 'starBase',
rna.expr = rnaExpr,
mir.expr = mirExpr)
ceOutput[1:5,]
3.2.3 Export ceRNAs network to Cytoscape
ceOutput2 <- ceOutput[ceOutputcorPValue<0.01 & ceOutput$regSim != 0,]
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)
3.3.6 Correlation plot on a local webpage
shinyCorPlot() , a interactive plot function based on shiny package, can be easily operated by just clicking the genes in each drop down box (in the GUI window). By running shinyCorPlot() function, a local webpage would pop up and correlation plot between a lncRNA and mRNA would be automatically shown.
shinyCorPlot(gene1 = rownames(deLNC),
gene2 = rownames(dePC),
rna.expr = rnaExpr,
metadata = metaMatrix.RNA)
