plotSpliceDGE: Differential splicing plot

In OliverVoogd/edgeR: Empirical Analysis of Digital Gene Expression Data in R

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

See Also

diffSpliceDGE, topSpliceDGE.

OliverVoogd/edgeR documentation built on July 28, 2022, 10:13 p.m.