plotSplice {limma} | R Documentation

## Differential splicing plot

### Description

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

### Usage

    plotSplice(fit, coef=ncol(fit), geneid=NULL, genecolname=NULL, rank=1L, FDR = 0.05)

### Arguments

`fit` | `MArrayLM` fit object produced by `diffSplice`.
`coef` | the coefficient (column) of fit for which differentially splicing is assessed.
`geneid` | character string, ID of the gene to plot.
`genecolname` | column name of `fit$genes` containing gene IDs. Defaults to `fit$genecolname`.
`rank` | integer, if `geneid=NULL` then this ranked gene will be plotted.
`FDR` | numeric, highlight exons as red dots with false discovery rate less than this cutoff. The FDR of the individual exon is calculated based on the exon-level t-statistics test for differences between each exon and all other exons for the same gene.

### 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 `diffSplice`. 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)

Gordon Smyth and Yifang Hu

### See Also

`diffSplice`, `topSplice`

A summary of functions available in LIMMA for RNA-seq analysis is given in 11.RNAseq.

### Examples

    # See diffSplice

[Package limma version 3.38.3 Index]