Plot exons of differentially expressed gene
Plot exons of differentially expressed gene and mark the differentially expressed exons.
plotExons(fit, coef = ncol(fit), geneid = NULL, genecolname = "GeneID",
exoncolname = NULL, rank = 1L, FDR = 0.05)fit |
|
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 |
exoncolname |
character string for the column name of |
rank |
integer, if |
FDR |
numeric, mark differentially expressed exons with false discovery rate less than this cutoff. |
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.
A plot is created on the current graphics device.
Yifang Hu and Gordon Smyth
A summary of functions available in LIMMA for RNA-seq analysis is given in 11.RNAseq.
## Not run: fit <- lmFit(y,design) fit <- eBayes(fit) plotExons(fit) plotExons(fit, exoncolname = "Start", rank = 1) plotExons(fit, geneid = "ps", genecolname = "Symbol", exoncolname = "Start") ## End(Not run)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.