gdcVolcanoPlot {GDCRNATools} | R Documentation |
A volcano plot showing differentially expressed genes/miRNAs
gdcVolcanoPlot(deg.all, fc = 2, pval = 0.01)
deg.all |
a dataframe generated from |
fc |
a numeric value specifying the threshold of fold change |
pval |
a nuemric value specifying the threshold of p value |
A volcano plot
Ruidong Li and Han Qu
genes <- c('ENSG00000231806','ENSG00000261211','ENSG00000260920', 'ENSG00000228594','ENSG00000125170','ENSG00000179909', 'ENSG00000280012','ENSG00000134612','ENSG00000213071') symbol <- c('PCAT7','AL031123.2','AL031985.3', 'FNDC10','DOK4','ZNF154', 'RPL23AP61','FOLH1B','LPAL2') group <- rep(c('long_non_coding','protein_coding','pseudogene'), each=3) logFC <- c(2.8,2.3,-1.1,1.9,-1.2,-1.6,1.5,2.1,-1.1) FDR <- rep(c(0.1,0.00001,0.0002), each=3) deg <- data.frame(symbol, group, logFC, FDR) rownames(deg) <- genes gdcVolcanoPlot(deg.all=deg)