gdcVolcanoPlot: Volcano plot of differentially expressed genes/miRNAs

In GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Description

A volcano plot showing differentially expressed genes/miRNAs

Usage

gdcVolcanoPlot(deg.all, fc = 2, pval = 0.01)

Arguments

deg.all	a dataframe generated from gdcDEAnalysis containing all genes of analysis no matter they are differentially expressed or not
fc	a numeric value specifying the threshold of fold change
pval	a nuemric value specifying the threshold of p value

Value

A volcano plot

Author(s)

Ruidong Li and Han Qu

Examples

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)

GDCRNATools documentation built on Nov. 27, 2020, 2 a.m.