plotExpr: Plot inferred gene structure and expression.

Description

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

Usage

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

Arguments

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

Methods

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.

Details

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.

Examples

Run this code

#See calcDenovo examples