specLSet-class: Class '"specLSet"'

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

Description

This class is used to store, show, and write generated results of the package.

Objects from the Class

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

Slots

input.parameter:

A list of parameter values.

ionlibrary:

A list of "specL" objects.

rt.normalized:

A numeric vector of normalized retention time values.

rt.input:

A numeric vector of retention time values.

Methods

show

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

summary

signature(x = "specLSet"): print summary of object content.

plot

signature(x = "specLSet"): plots normalized versus input rt.

write.spectronaut

signature(x = "specLSet"): writes object to ASCII file.

generate.consensus

signature(x = "specLSet"): generates consensus specLSet object by combining all specL objects having a redundant group_id which is defined by paste([e-mail]_silico, x@peptideModSeq, sep='_').

merge.specLSet

signature(x = "specLSet"): merges two specLSet objects.

ionlibrary

signature(x = "specLSet"): returns a list of specL objects.

rt.input

signature(x = "specLSet"): returns a numeric vector of input rt values.

rt.normalized

signature(x = "specLSet"): returns a numeric vector of normalized rt values.

getProteinPeptideTable

signature(x = "specLSet"): returns table of peptide protein mappings.

Note

No notes yet.

Author(s)

Christian Panse 2014

See Also

genSwathIonLib

Examples

    showClass("specL")
    showClass("specLSet")

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