plotSpliceDGE: Differential splicing plot

Description Usage Arguments Details Value Author(s) See Also

Description

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

Usage

1
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.



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