parameters: Creates and manipulates parameter objects for rTANDEM

In rTANDEM: Interfaces the tandem protein identification algorithm in R

Description

Those functions instantiate parameter objects for rTANDEM and manipulate their values. Many of those functions give default values, either for general settings (e.g. setParamDefault), for instrument specific settings (e.g. setParamOrbitrap), or for function specific settings (e.g. setParamPTMTreeSearch).

Usage

rTParam()
setParamValue(param, category, parameter=NULL, value)
setParamDefault(param=NULL)
setParamPTMTreeSearch(param=NULL)
setParamOrbitrap(param=NULL)
setParamIonTrap(param=NULL)
setParamQuadTof05da(param=NULL)
setParamQuadTof100ppm(param=NULL)
rTTaxo(taxon=NA, format=NA, URL=NA)
addTaxon(taxonomy=NULL, taxon, format="peptide", URL)
## S3 method for class 'rTParam'
print(x, ...)

Arguments

param	A parameter object of class rTParam.
x	A parameter object of class rTParam.
...	Further arguments passed to or from other methods.
category	A string representing a category of parameters (e.g. "output", "protein").
parameter	A string representing the name of a parameter.
value	The value to give to the parameter.
taxon	A string representing the name of a taxon (e.g. "homo sapiens").
taxonomy	A taxonomy object of class rTTaxo.
format	A string representing the type of the database. The four types are: "peptide", "saps", "mods" and "spectrum".
URL	A string representing the full path to the database file.

Value

The functions rTParam, and all functions setParam..., return an object of S3 class rTParam. The functions rTTaxo and addTaxon return an object of S3 class rTTaxo. print.rTParam is used for its side effect of displaying a parameter object.

References

thegpm.org/TANDEM/api/

See Also

GetParamFromXML, GetTaxoFromXML, WriteTaxoToXML, WriteParamToXML.

Examples

# Initialize an empty parameter object:
param <- rTParam()
print.rTParam(param)

# Set general values.
param <- setParamDefault(param)

# Add instrument specific values for a LTQ mass spectrometer.
param <- setParamIonTrap(param)
print.rTParam(param)

Example output

Loading required package: XML
Loading required package: Rcpp
Loading required package: data.table
rTParam object with 0 defined parameters.

rTParam object with 41 defined parameters.

output, histogram column width: 
	30

output, histograms: 
	yes

output, maximum valid expectation value: 
	0.1

output, parameters: 
	yes

output, path: 
	rTANDEM.xml

output, path hashing: 
	yes

output, performance: 
	yes

output, proteins: 
	yes

output, results: 
	valid

output, sort results by: 
	protein

output, sequences: 
	yes

output, spectra: 
	yes

output, xsl path: 
	/usr/local/lib/R/site-library/rTANDEM/extdata/tandem-style.xsl

protein, cleavage site: 
	[RK]|{P}

protein, C-terminal residue modification mass: 
	0

protein, N-terminal residue modification mass: 
	0

refine, maximum valid expectation value: 
	0.1

refine, point mutations: 
	no

refine, potential modification mass: 
	15.994915@M,0.9848@N,0.9848@Q

refine: 
	yes

refine, spectrum synthesis: 
	yes

refine, unanticipated cleavage: 
	yes

refine, use potential modifications for full refinement: 
	no

residue, modification mass: 
	57.021464@C

residue, potential modification mass: 
	15.994915@M

scoring, maximum missed cleavage sites: 
	1

scoring, minimum ion count: 
	4

spectrum, dynamic range: 
	100

spectrum, fragment monoisotopic mass error: 
	0.4

spectrum, fragment monoisotopic mass error units: 
	Daltons

spectrum, minimum fragment mz: 
	150

spectrum, minimum peaks: 
	15

spectrum, minimum parent m+h: 
	500

spectrum, parent monoisotopic mass error minus: 
	0.5

spectrum, parent monoisotopic mass error plus: 
	3

spectrum, parent monoisotopic mass error units: 
	Daltons

spectrum, parent monoisotopic mass isotope error: 
	no

spectrum, threads: 
	1

spectrum, total peaks: 
	50

spectrum, use noise suppression: 
	no

spectrum, maximum parent charge: 
	4

rTANDEM documentation built on April 28, 2020, 7:04 p.m.