lpm_refine: Refine 'pepmatched' objects.

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

Description

This function allows to make subselections of a pepmatched object with cutoffs for different parameters. In this way, the pepmatch function itself only has to be run once with not to strict parameters, and analysis can afterwards be refined. Notice that it is impossible to refine parameters to less strict values than the ones used to generate the pepmatched object.

Usage

lpm_refine(pepmatched_object, labelthresh, elutionthresh, MWmin, MWmax,
  quantmin, quantmax, labelcountmin, labelcountmax, zmin, zmax,
  remove.more.labels.than.charges = F, remove.run = NULL,
  only.identified = FALSE)

Arguments

pepmatched_object	Object of class pepmatched that you want to trim.
labelthresh	Numeric. Threshold for molecular weight difference (in Dalton) between to peaks to differ from theoretical mass difference between two labelled peptides. Regardless of number of labels.
elutionthresh	Numeric. Threshold for elution time difference between two peaks to be considered a peakpair.
MWmin	Numeric. Minimal molecular weight of the peptide without labels.
MWmax	Numeric. Maximal molecular weight of the peptide without labels.
quantmin	Numeric vector of one or two elements. Minimal untransformed quantity for a feature to be retained. The highest value of the vector is the cutoff for the most abundant peak in a pair, the lowest for the least abundant. If you want to make sure you pick up extreme up-or downregulations, the vector should contain one zero or very small number. If you want to discart a peak pair once one of the peaks is below a quantity threshold, you can set the threshold with one minimal value (a vector with one element). This is equivalent to a vector with two equal elements.
quantmax	Numeric. Maximal quantity (intensity or abundance). This is an AND function, so both peaks in a peak pair have to be above this quantity in order to be discarted.
labelcountmin	Integer. Minimal number of labels.
labelcountmax	Integer. Maximal number of labels.
zmin	Integer. Minimal number of charges.
zmax	Integer. Maximal number of charges.
remove.more.labels.than.charges	Logical. Remove features that have more labels than charges. This is usually relevant since most labels are charged, so finding a peptide that has more labels than charges is often impossible.
remove.run	Integer. A single value or a vector of runnumbers that should be discarted.
only.identified	Logical. Only features that have been identified with mass match are retained.

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