AnalyzeSimulatedData: Analyze simulation reslts
In chrismckennan/MSeQUiP: Quantifying uncertainty in peptide-spectrum matches

Analyze results derived from simulated data.

AnalyzeSimulatedData(
  Sim,
  Forward,
  Reverse,
  pi0 = NULL,
  psm.fdr.bin = c(0, 0.01, 0.05, seq(0.1, 1, by = 0.1))
)

`Sim`	Simulation output from `SimulateDataPaper`
`Forward`	Target search results from `PerformSearch`
`Reverse`	Decoy search results from `PerformSearch`
`pi0`	If known, the fraction of simulated spectra whose generating analyte does not lie in the target database. Detault is `NULL`, i.e. unknown
`psm.fdr.bin`	PSM-fdr bins to determine PSM-fdr calibration

A list

`S.F`	Bayes factor score for target database
`S.R`	Bayes factor score for reverse database
`SEE.F`	Score-ordering error rate
`Sfdr`	DI-fdr
`PSMfdr`	PSM-fdr
`pi0.hat`	Estimate for pi0
`pvalues`	p-values for the null hypothesis that the spectrum was not generated by an analyte in the target database
`Pep.F`	Inferred target peptide
`Correct`	Is `Pep.F` correct
`PSMfdr.bins`	PSM-fdr calibration results