specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Documentation for package ‘specL’ version 1.0.0

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annotateProteinID	annotateProteinID
BiblioSpec	BiblioSpec Reader
bibliospec	BiblioSpec Reader
genSwathIonLib	Spectrum library generator for SWATH analysis
ionlibrary	Class '"specLSet"'
ionlibrary-method	Class '"specLSet"'
iRT	iRT peptides - independent retention time peptides
irt	iRT peptides - independent retention time peptides
iRTpeptides	iRT peptides - independent retention time peptides
MRM	Spectrum library generator for SWATH analysis
peptideStd	Peptide standard
peptideStd.redundant	Peptide standard
plot	Class '"specLSet"'
plot,specL-methods	Method for Function 'plot' in Package 'specL'
plot,specLSet-methods	Method for Function 'plot' in Package 'specL'
plot-method	Method for Function 'plot' in Package 'specL'
plot-method	Class '"specL"'
plot-method	Class '"specLSet"'
plot-methods	Method for Function 'plot' in Package 'specL'
read.bibliospec	BiblioSpec Reader
rt.input	Class '"specLSet"'
rt.input-method	Class '"specLSet"'
rt.normalized	Class '"specLSet"'
rt.normalized-method	Class '"specLSet"'
show-method	Methods for Function 'show' in Package 'specL' ~~
show-method	Class '"specL"'
show-method	Class '"specLSet"'
show-methods	Methods for Function 'show' in Package 'specL' ~~
Skyline	BiblioSpec Reader
skyline	BiblioSpec Reader
specL	Spectrum library generator for SWATH analysis
specL-class	Class '"specL"'
specLSet-class	Class '"specLSet"'
SWATH	Spectrum library generator for SWATH analysis
swath	Spectrum library generator for SWATH analysis
write.Spectronaut	Methods for Function 'write.Spectronaut' in Package 'specL'
write.Spectronaut,specL-methods	Methods for Function 'write.Spectronaut' in Package 'specL'
write.Spectronaut,specLSet-methods	Methods for Function 'write.Spectronaut' in Package 'specL'
write.Spectronaut-method	Class '"specL"'
write.Spectronaut-method	Class '"specLSet"'
write.Spectronaut-method	Methods for Function 'write.Spectronaut' in Package 'specL'