plotMA {bakR} | R Documentation |
This function outputs a L2FC(kdeg) MA plot. Plots are colored according to statistical significance and the sign of L2FC(kdeg)
plotMA(
obj,
Model = c("MLE", "Hybrid", "MCMC"),
FDR = 0.05,
Exps = 2,
Exp_shape = FALSE
)
obj |
Object of class bakRFit outputted by |
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 |
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.
# 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")