plotGene: Plot the pre-modeled and modeled profiles for one gene

In ste-depo/INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

Description

A method to see the shapes of the estimated synthesis, degradation and processing rates, pre-RNA and total RNA concentrations (solid thin lines) their variances (dashed lines) and the modeled rates and concentrations (ticker solid line) of a single gene.

Usage

plotGene(
  object,
  ix,
  relative_expression = FALSE,
  fix.yaxis = FALSE,
  priors = TRUE,
  constantModel = FALSE
)

## S4 method for signature 'INSPEcT'
plotGene(
  object,
  ix,
  relative_expression = FALSE,
  fix.yaxis = FALSE,
  priors = TRUE,
  constantModel = FALSE
)

Arguments

object	An object of class INSPEcT
ix	Eiher a rowname or a row number to select one single gene
relative_expression	A logical, indicating whether expressions are rates should be plotted relative to their initial value (Default=FALSE).
fix.yaxis	A logical, indicating whether the limits for y-axis of degradation and processing rates should be fixed relative to their distributions
priors	A logical, if true the priors of the rates are plotted
constantModel	A logical, if true the constant model for the + nascent modeling are shown

Value

A list containing total RNA levels and their confidence interval (levels plus and minus one standard deviation), pre-RNA lelevs and their confidence intervals, synthsis rates and their confidence intervals, degradation rates and processing rates of the selected gene.

Examples

nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
plotGene(nascentInspObj10, 1)

ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.