specL-class: Class '"specL"'

In specL: specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Description

This class is used to store, print, and plot the generated results of the package.

Objects from the Class

Objects can be created by calls of the form new("specL", ...).

Slots

group_id:

Object of class "character" just an id

peptide_sequence:

Object of class "character" AA sequence

proteinInformation:

Object of class "character" a string contains the protein identifier.

q1:

Object of class "numeric" peptide weight m/Z as measured by the MS device

q1.in_silico:

Object of class "numeric" peptide weight m/Z computed in-silico.

q3:

Object of class "numeric" measured fragment ions.

q3.in_silico:

Object of class "numeric" in-silico derived fragment ions.

score:

Object of class "numeric" taken from bibliospec - psm score

prec_z:

Object of class "numeric" pre-cursor charge.

frg_type:

Object of class "character" fragmenbt ion type, e.g., b or y ion.

frg_nr:

Object of class "numeric" fragment ion number

frg_z:

Object of class "numeric" fragment ion charge.

relativeFragmentIntensity:

Object of class "numeric" percentage base peaks of frament ions.

irt:

Object of class "numeric" independent retention time in seconds.

peptideModSeq:

Object of class "numeric" a vector contains the mass diff between AA and mod AA.

mZ.error:

Object of class "numeric" a string contains the protein identifier.

filename:

Object of class "character" a string contains the filename of the ions.

Methods

plot

signature(x = "specL"): plots the fragment ions of specL object.

show

signature(x = "specL"): shows the content of specL object.

write.spectronaut

signature(x = "specL"): writes the specL object to a ASCII file.

Note

No notes yet.

Author(s)

Christian Panse 2014

See Also

genSwathIonLib

Examples

    showClass("specL")

specL documentation built on Nov. 8, 2020, 7:55 p.m.