AnnoVolcanoPlot {MARVEL} | R Documentation |
Annotate volcano plot with nonsense-mediated decay (NMD) genes
Description
Annotate volcano plot generated from differential gene expression analysis with genes predicted to undergo splicing-induced NMD.
Usage
AnnoVolcanoPlot(
MarvelObject,
anno = FALSE,
anno.gene_short_name = NULL,
label.size = NULL,
point.size = 1,
xlabel.size = 8
)
Arguments
MarvelObject |
Marvel object. S3 object generated from |
anno |
Logical value. If set to |
anno.gene_short_name |
Vector of character strings. When |
label.size |
Numeric value. When |
point.size |
Numeric value. Size of data points. Default value is |
xlabel.size |
Numeric value. Font size of the xtick labels. Default is |
Value
An object of class S3 with new slots MarvelObject$NMD$AnnoVolcanoPlot$Table
and MarvelObject$NMD$AnnoVolcanoPlot$Plot
.
Examples
marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))
marvel.demo <- AnnoVolcanoPlot(MarvelObject=marvel.demo)
# Check outputs
head(marvel.demo$NMD$AnnoVolcanoPlot$Table)
marvel.demo$NMD$AnnoVolcanoPlot$Plot
[Package MARVEL version 1.4.0 Index]