gdcVolcanoPlot {GDCRNATools} | R Documentation

## Volcano plot of differentially expressed genes/miRNAs

### 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)

[Package GDCRNATools version 1.14.0 Index]