Description Usage Arguments Details Value Author(s) See Also Examples
Plot differential usage results by exons and junctions for the specified gene and highlight the significantly spliced exons and junctions.
1 | plotExonJunc(fit, coef=ncol(fit), geneid, genecolname=NULL, FDR=0.05, annotation=NULL)
|
fit |
|
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 |
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 |
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.
A plot is created on the current graphics device.
Yunshun Chen and Gordon Smyth
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## 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)
|
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