plotExonJunc: Differential splicing plot with junctions

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plotExonJunc.R

Description

Plot differential usage results by exons and junctions for the specified gene and highlight the significantly spliced exons and junctions.

Usage

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plotExonJunc(fit, coef=ncol(fit), geneid, genecolname=NULL, FDR=0.05, annotation=NULL)

Arguments

fit

MArrayLM fit object produced by diffSplice. Must have the Entrez gene ids for all the exons and junctions stored in fit$genes$GeneID, length information for all the exons and junctions stored in fit$genes$Length and the strand information stored in fit$genes$Strand. To distinguish between exons and junctions, fit$genes$Length has to be set to 1 for all the junctions.

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 geneid.

FDR

numeric, highlight exons and junctions with false discovery rate less than this cutoff. Red indicates up-regulation whereas blue indicates down-regulation. The FDR of the individual exon/junction is calculated based on the exon-level t-statistics test for differences between each exon/junction and all other exons/junctions for the same gene.

annotation

data frame containing the full exon annotation of the corresponding species. Must have the Entrez gene ids for all the exons stored in the GeneID column, start and end positions for all the exons stored in the Start and End columns, respectively.

Details

Plot differential usage results by exons and junctions for the specified gene. The significantly spliced individual exons are highlighted as red blocks if up-regulated and blue blocks if down-regulated. All other exons are displayed as black blocks. The significantly spliced individual junctions are highlighted as red lines if up-regulated and blue lines if down-regulated. All other junctions are displayed as black lines.

Since the diffSplice analysis is usually performed after filtering, the full annotation (e.g. the inbuilt annotation in featureCounts) is highly recommended for producing the plot. When annotation is provided, the filtered exons are displayed as grey blocks.

Value

A plot is created on the current graphics device.

Author(s)

Yunshun Chen and Gordon Smyth

See Also

diffSplice, topSplice

Examples

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## Not run: 
# diffSplice analysis
v <- voom(dge, design)
fit <- lmFit(v, design)
ex <- diffSplice(fit, geneid="GeneID")

# Get full annotation from Rsubread
library(Rsubread)
annotation.full <- getInBuiltAnnotation("mm10")

# Make a plot
plotExonJunc(ex, geneid="Foxp1", genecolname="Symbol", annotation=annotation.full)

## End(Not run)

hdeberg/limma documentation built on Dec. 20, 2021, 3:43 p.m.