SimulateDataPaper: Simulate data from the paper
In chrismckennan/MSeQUiP: Quantifying uncertainty in peptide-spectrum matches

Description Usage Arguments Value

View source: R/SimulateNull.R

Simulate MS/MS spectra subject to score-ordering and database incompleteness errors. The former contain simulated signal and real noise peaks, and the latter are real spectra whose precursors have been shifted +/-10m/z.

1	SimulateDataPaper(ProcessedDataPath, n.null, t.df.by = 4, list.train.paths)

`ProcessedDataPath`	Path to processed data.
`n.null`	Number of spectra to simulate subject to database incompleteness errors.
`t.df.by`	Log-signal intensity errors are drawn from a t distribution with `t.df.by` degrees of freedom.

A list.

`Spectra.sim`	A list of simulated spectra. It is assumed each MS/MS peak's charge is unknown in these simulations.
`Headers.sim`	Headers for the simulated spectra
`Pep`	Generating peptide
`Charge`	Precursor charge
`Scale`	The intensity scale for each simulated spectrum