gdcBarPlot: Bar plot of differentially expressed genes/miRNAs

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

Description

A bar plot showing the number of down-regulated and up-regulated DE genes/miRNAs of different biotypes

Usage

gdcBarPlot(deg, angle = 0, data.type)

Arguments

deg	a dataframe generated from gdcDEReport containing DE genes/miRNAs ids, logFC, etc.
angle	a numeric value specifying the angle of text on x-axis. Default is 0
data.type	one of 'RNAseq' and 'miRNAs'

Value

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

Jialab-UCR/GDCRNATools documentation built on Nov. 28, 2020, 11:23 a.m.