plotSpliceDGE: Differential splicing plot
In hiraksarkar/edgeR_fork: Empirical Analysis of Digital Gene Expression Data in R

Description Usage Arguments Details Value Author(s) See Also

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

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

`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.

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.

A plot is created on the current graphics device.

Yunshun Chen, Yifang Hu and Gordon Smyth

diffSpliceDGE, topSpliceDGE.

hiraksarkar/edgeR_fork documentation built on Dec. 20, 2021, 3:52 p.m.