make.statlist: Reorganize a 'pepmatched' object into matrix format.

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

Description

This function takes an object of class pepmatched and transforms it to class lpm_statlist. This statlist is a format that is suited for statistical analysis. It also contains the same trimming parameters as the lpm_refine function.

Usage

make.statlist(pepmatched_object, cutoff = 1, logtransform = T, 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.
cutoff	Numeric. Proportion of runs in which a feature should be found to be retained in statlists. Default is 1
logtransform	Logical. Should the data be log2 transformed? Set to FALSE if data are already transformed in earlier step, or if you want to manually transform your data. Otherwise this is the best place to log2 transform your data.
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. Minimal quantity (intensity or abundance). This is an AND function, so both peaks in a peak pair have to be below this quantity in order to be discarted.
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.

Value

An object of class lpm_statlist

Author(s)

Rik Verdonck

See Also

lpm_refine lpm_make.RGList

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