specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

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Documentation for package ‘specL’ version 1.39.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

annotate.protein_id	Annotate protein_id
BiblioSpec	BiblioSpec Reader
bibliospec	BiblioSpec Reader
cdsw	Generate Dynamic SWATH Window
generate.consensus	Class '"specLSet"'
generate.consensus-method	Class '"specLSet"'
generateDynamicSwathWindow	Generate Dynamic SWATH Window
genSwathIonLib	Spectrum library generator for SWATH analysis
getProteinPeptideTable	Class '"specLSet"'
getProteinPeptideTable-method	Class '"specLSet"'
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
merge.specLSet	Class '"specLSet"'
merge.specLSet-method	Class '"specLSet"'
MRM	Spectrum library generator for SWATH analysis
ms1.p2069	ms1 mass
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'
plot.psm	BiblioSpec Reader
plot.psmSet	BiblioSpec Reader
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"'
summary-method	Class '"specLSet"'
summary.psmSet	BiblioSpec Reader
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'