plotMA: Creating L2FC(kdeg) MA plot from fit objects

In bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

Creating L2FC(kdeg) MA plot from fit objects

Description

This function outputs a L2FC(kdeg) MA plot. Plots are colored according to statistical significance and the sign of L2FC(kdeg)

Usage

plotMA(
  obj,
  Model = c("MLE", "Hybrid", "MCMC"),
  FDR = 0.05,
  Exps = 2,
  Exp_shape = FALSE
)

Arguments

obj	Object of class bakRFit outputted by bakRFit function
Model	String identifying implementation for which you want to generate an MA plot
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 log-10 transformed replicate average read counts, y-axis is the log-2 fold-change in the degradation rate constant.

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
plotMA(Fit, Model = "MLE")

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