rTResult-class: Class "rTResult" and "rTResult_s"

In rTANDEM: Interfaces the tandem protein identification algorithm in R

Description

A rTResult object is designed to contain the information of a X!Tandem analysis and allow data mining of this information. rTResult_s is a sub-class that adds a data.table slot for holding spectra.

Objects from the Class

Objects can be created by calls to new("rTResult", ...) or new("rTResult_s", ...).

Slots

result.file:

Object of class "character" ~~

proteins:

Object of class "data.table" ~~

peptides:

Object of class "data.table" ~~

ptm:

Object of class "data.table" ~~

spectra:

Object of class "data.table" ~~

used.parameters:

Object of class "data.frame" ~~

unused.parameters:

Object of class "vector" ~~

sequence.source.paths:

Object of class "vector" ~~

estimated.false.positive:

Object of class "integer" ~~

total.peptides.used:

Object of class "integer" ~~

total.proteins.used:

Object of class "integer" ~~

total.spectra.assigned:

Object of class "integer" ~~

total.spectra.used:

Object of class "integer" ~~

total.unique.assigned:

Object of class "integer" ~~

start.time:

Object of class "character" ~~

xtandem.version:

Object of class "character" ~~

quality.values:

Object of class "vector" ~~

nb.input.models:

Object of class "integer" ~~

nb.input.spectra:

Object of class "integer" ~~

nb.partial.cleavages:

Object of class "integer" ~~

nb.point.mutations:

Object of class "integer" ~~

nb.potential.C.terminii:

Object of class "integer" ~~

nb.potential.N.terminii:

Object of class "integer" ~~

nb.unanticipated.cleavages:

Object of class "integer" ~~

initial.modelling.time.total:

Object of class "numeric" ~~

initial.modelling.time.per.spectrum:

Object of class "numeric" ~~

load.sequence.models.time:

Object of class "numeric" ~~

refinement.per.spectrum.time:

Object of class "numeric" ~~

Methods

No methods defined with class "rTResult" in the signature.

Author(s)

Authors: Frederic Fournier, Charles Joly Beauparlant, Rene Paradis, Arnaud Droit Maintainer: Frederic Fournier <[e-mail]>, Charles Joly Beauparlant <[e-mail]>

Examples

showClass("rTResult")

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