Creating L2FC(kdeg) MA plot from fit objects

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

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

# Fit data with fast implementation
Fit <- bakRFit(sim$bakRData)
#> Finding reliable Features
#> Filtering out unwanted or unreliable features
#> Processing data...
#> Estimating pnew with likelihood maximization
#> Estimating unlabeled mutation rate with -s4U data
#> Estimated pnews and polds for each sample are:
#> # A tibble: 4 × 4
#> # Groups:   mut [2]
#>     mut  reps   pnew     pold
#>   <int> <dbl>  <dbl>    <dbl>
#> 1     1     1 0.0500 0.000999
#> 2     1     2 0.0500 0.000999
#> 3     2     1 0.0501 0.000999
#> 4     2     2 0.0501 0.000999
#> Estimating fraction labeled
#> Estimating per replicate uncertainties
#> Estimating read count-variance relationship
#> Averaging replicate data and regularizing estimates
#> Assessing statistical significance
#> All done! Run QC_checks() on your bakRFit object to assess the 
#>             quality of your data and get recommendations for next steps.

# Volcano plot
plotMA(Fit, Model = "MLE")


# }