plotVolcano: Creating L2FC(kdeg) volcano plot from fit objects

In bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

Creating L2FC(kdeg) volcano plot from fit objects

Description

This function creates a L2FC(kdeg) volcano plot. Plots are colored according to statistical significance and sign of L2FC(kdeg).

Usage

plotVolcano(obj, FDR = 0.05, Exps = 2, Exp_shape = FALSE)

Arguments

obj	Object contained within output of bakRFit. So, either Fast_Fit (MLE implementation fit), Stan_Fit (MCMC implementation fit), or Hybrid_Fit (Hybrid implementation fit)
FDR	False discovery rate to control at for significance assessment
Exps	Vector of Experimental IDs to include in plot; must only contain elements within 2:(# of experimental IDs). If NULL, data for all Experimental IDs is plotted.
Exp_shape	Logical indicating whether to use Experimental ID as factor determining point shape in volcano plot

Value

A ggplot object. Each point represents a transcript. The x-axis is the log-2 fold change in the degradation rate constant and the y-axis is the log-10 transformed multiple test adjusted p value.

Examples

# Simulate data for 500 genes and 2 replicates
sim <- Simulate_bakRData(500, nreps = 2)

# Fit data with fast implementation
Fit <- bakRFit(sim$bakRData)

# Volcano plot
plotVolcano(Fit$Fast_Fit)

bakR documentation built on June 22, 2024, 6:55 p.m.