specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

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Documentation for package ‘specL’ version 1.12.0

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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'