edgeR: plotSpliceDGE – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

edgeR

plotSpliceDGE

Differential splicing plot

Description

Plot relative log-fold changes by exons for the specified gene and highlight the significantly spliced exons.

Usage

plotSpliceDGE(lrt, geneid=NULL, genecolname=NULL, rank=1L, FDR=0.05)

Arguments

`lrt`	`DGELRT` object produced by `diffSpliceDGE`.
`geneid`	character string, ID of the gene to plot.
`genecolname`	column name of `lrt$genes` containing gene IDs. Defaults to `lrt$genecolname`.
`rank`	integer, if `geneid=NULL` then this ranked gene will be plotted.
`FDR`	numeric, mark exons with false discovery rate less than this cutoff.

Details

Plot relative log2-fold-changes by exon for the specified gene. The relative logFC is the difference between the exon's logFC and the overall logFC for the gene, as computed by diffSpliceDGE. The significantly spliced individual exons are highlighted as red dots. The size of the red dots are weighted by its significance.

Value

A plot is created on the current graphics device.

Author(s)

Yunshun Chen, Yifang Hu and Gordon Smyth