plotExpr: Plot inferred gene structure and expression.
In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description Usage Arguments Details Methods Examples

Plots variants with sufficiently large posterior probability of being expressed along with their (marginal) estimated expression.

1 2	plotExpr(gene, minProbExpr = 0.5, minExpr = 0.1, xlab = "(kb)", ylab = "", xlim, cex = 1, yaxt = "n", col, ...)

`gene`	`denovoGeneExpr` object containing results for a single gene, as returned by `calcDenovo`.
`minProbExpr`	Variants with marginal posterior probability of expression below `minProbExpr` are not reported
`minExpr`	Variants with (marginal) estimated expression below `minExpr` are not reported. Can be useful to remove sequence preference artifacts.
`xlab`	x-axis label, passed on to `plot`
`ylab`	y-axis label, passed on to `plot`
`xlim`	x-axis limits, passed on to `plot`
`cex`	Character expansion, passed on to `plot`
`yaxt`	Type of y-axis, passed on to `plot`
`col`	Colors for each variant, defaults to rainbow colors. It is possible to specify a single color.
`...`	Other arguments to be passed on to `plot`

The marginal posterior probability that a variant is expressed is the sum of the posterior probabilities of all models containing that variant.

The marginal estimated expression is the average expression across all models (including those where the variant has 0 expression) weighted by the posterior probability of each model.

signature(gene = "denovoGeneExpr"): gene contains the results from a de novo isoform expression analysis for a single gene, as returned by calcDenovo. When calcDenovo is run on multiple genes simultaneously, the desired gene can be selected using the "[[" operator as usual.