lpm_mockdata: Generate mock data.

In goat-anti-rabbit/labelpepmatch.R: Tools For Interpreting Mass Spectra With Labeled Peptides

Description

Generates mock data on the basis of an lpm_input object. This function is integrated in pepmatch FDR estimation with its default parameters. The use outside of the pepmatch function is only advised if you want to explore this function, or if you want to use non-default parameters. The way this function works, is by chopping up values of masses (or actually of m/z) and retention times, randomizing them, and pasting them back together. This is important since mass/charge values are non-random (since masses are often close to integer values) and also the coupling of retention time with mass/charge is non-random. For example, mass values 1155.2 and 2456.2 will be reshuffled to 1456.2 and 2115.2 with a masslevel of 1000.

Usage

lpm_mockdata(input, masslevel = 100, retlevel = 3,
  elutionunit = "minutes", graphics = F)

Arguments

input	An object of class lpm_input
masslevel	Numeric. Level at which the mass values should be shopped up.
retlevel	Numeric. Level at which the retention time values should be shopped up. Careful: it is best to either use small values (like up to maximum 10% of the range of retention times) for a tight coupling between m/z and retention time, or a value that is larger than the maximum retention time for a loose coupling between m/z and retention time. Intermediate values will chop up your data in chunks. Have a look at it with the graphics parameter on.
elutionunit	Character. Sketchy. Default is "minutes", alternative is "seconds".
graphics	Output a plot of the mock database versus the real database.

Value

An object of class lpm_input. The values for m/z and retention time are shuffeled. The quantity values are all set to 0.

Author(s)

Rik Verdonck

See Also

pepmatch

goat-anti-rabbit/labelpepmatch.R documentation built on May 17, 2019, 7:29 a.m.