S3 plot function for FDR assessment result arrays — plot.fdr

This function creates standard plots from result arrays as produced by e.g. the function assess_fdr_byrun(), visualizig assay, peptide and protein level FDR for each run at m-score cutoffs 1e-2 and 1e-3. Furthermore, Target and Decoy ID numbers are visualized.

# S3 method for fdr_cube
plot(
  x,
  output = "Rconsole",
  filename = "FDR_report_byrun",
  plot_mscore_levels = c(0.01, 0.001),
  ...
)

Arguments

x: Array of by-run FDR assessment results as produced e.g. by the function assess_fdr_byrun() from this package.
output: Choose output type. "pdf_csv" creates the output as files in the working directory, "Rconsole" triggers delivery of the output to the console enabling further computation and/or custom plotting / output.
filename: Basename for output files to be created (if output = "pdf_csv" has been selected).
plot_mscore_levels: Define m-score levels to plot the estimated FDR results.
...: Extra arguments passed on to functions inside this.

Value

Plots in Rconsole or report files.

Author

Moritz Heusel

Examples

{
 data("OpenSWATH_data", package="SWATH2stats")
 data("Study_design", package="SWATH2stats")
 data <- sample_annotation(OpenSWATH_data, Study_design)
 x <- assess_fdr_byrun(data, FFT=0.7, output="Rconsole", plot=FALSE)
 retlist <- plot(x, output="Rconsole", filename="Assess_fdr_byrun_testplot",
                          plot_mscore_levels=0.01)
 }
#> The average FDR by run on assay level is 0.003
#> The average FDR by run on peptide level is 0.004
#> The average FDR by run on protein level is 0.07