classes: rTANDEM S3 and S4 classes

In CharlesJB/rTANDEM: Encapsulate X!Tandem in R.

Description

The functions rTParam() and rTTaxo() instantiate S3 object of respective class 'rTParam' and 'rTTaxo', while setParamValue() helps set the value of a given parameter in an existing rTParam object. 'rTParam' and 'rTTaxo' are data.frame specifically structured to be used by the other functions of the rTANDEM package. rTResult is an S4 class structured to hold the results of the analysis.

Usage

rTParam()
rTTaxo(taxon=NA, format=NA, URL=NA)
setParamValue(param, category, parameter, value)

Arguments

param	A rTParam object.
category	The category of an x!tandem full parameter. For example 'output' in "output, histograms" or 'protein' in "protein, cleavage site".
parameter	The specific parameter of an x!tandem full parameter. For example, 'histograms' in "output, histograms", or 'cleavage site' in "protein, cleavage site".
value	The value to be assigned to the full parameter of the rTParam object.
taxon	An optional string or vector containing the name(s) of the taxa corresponding to the database files, for example, 'yeast' or 'Homo sapiens'.
format	An optional string or vector containing the types of the database files: 'peptide', 'saps', 'mods' or 'spectrum'.
URL	An optional string of vector containing the paths of the database files.

CharlesJB/rTANDEM documentation built on May 6, 2019, 9:58 a.m.