limma (version 3.28.6)

plotExons: Plot exons of differentially expressed gene

Description

Plot exons of differentially expressed gene and mark the differentially expressed exons.

Usage

plotExons(fit, coef = ncol(fit), geneid = NULL, genecolname = "GeneID",
          exoncolname = NULL, rank = 1L, FDR = 0.05)

Arguments

fit

MArrayLM fit object produced by eBayes.

coef

the coefficient (column) of fit for which differential expression is assessed.

geneid

character string, ID of the gene to plot.

genecolname

character string for the column name of fit$genes containing gene IDs. Defaults to "GeneID" for Entrez Gene ID.

exoncolname

character string for the column name of fit$genes containing exon IDs.

rank

integer, if geneid=NULL then this ranked gene will be plotted.

FDR

numeric, mark differentially expressed exons with false discovery rate less than this cutoff.

Value

• A plot is created on the current graphics device.

Details

Plots log2-fold-change by exon for the specified gene and highlight the differentially expressed exons. Show annotations such as GeneID, Symbol and Strand if available as title for the gene to plot. The significantly differentially expressed individual exons are highlighted as red dots for up-regulation and as blue dots for down-regulation. The size of the dots are weighted by its significance.

See Also

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

Examples

fit <- lmFit(y,design)
fit <- eBayes(fit)
plotExons(fit)
plotExons(fit, exoncolname = "Start", rank = 1)
plotExons(fit, geneid = "ps", genecolname = "Symbol", exoncolname = "Start")