# specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

## Documentation for package ‘specL’ version 1.30.0

- 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'