isobar-package	isobar-package
%inrange%	utils
adjust.ratio.pvalue	calculate-pvalues
as.data.frame,IBSpectra-method	IBSpectra-class
as.data.frame,ProteinGroup-method	ProteinGroup-class
as.data.frame.IBSpectra	IBSpectra-class
as.data.frame.ProteinGroup	ProteinGroup-class
calc.delta.score	calc.delta.score
calc.pep.delta.score	calc.delta.score
calcPeptidePosition	calc.startpos
calcProbXDiffNormals	distr-methods
calcProbXGreaterThanY	distr-methods
calculate.dNSAF	calculate.dNSAF
calculate.emPAI	calculate.emPAI
calculate.mult.sample.pvalue	calculate-pvalues
calculate.ratio.pvalue	calculate-pvalues
calculate.sample.pvalue	calculate-pvalues
class:IBSpectra	IBSpectra-class
class:NoiseModel	NoiseModel-class
class:ProteinGroup	ProteinGroup-class
classLabels	IBSpectra-class
classLabels,IBSpectra-method	IBSpectra-class
classLabels<-	IBSpectra-class
classLabels<-,IBSpectra-method	IBSpectra-class
coerce,data.frame,ProteinGroup-method	ProteinGroup-class
coerce,IBSpectra,data.frame-method	IBSpectra-class
combn.matrix	ratio-summ
combn.protein.tbl	ratio-summ
connect.nodes	isobar-reports
correct.peptide.ratios	correct.peptide.ratios
correctIsotopeImpurities	isobar-preprocessing
correctIsotopeImpurities,IBSpectra-method	isobar-preprocessing
create.meta.reports	isobar-reports
create.reports	isobar-reports
distrprint	distr-methods
do.log	isobar-log
do.log,IBSpectra,character-method	isobar-log
draw.boxplot	isobar-reports
draw.protein.group	isobar-reports
draw.proteingroup.row	isobar-reports
estimateRatio	isobar-analysis
estimateRatio,IBSpectra,ANY,character,character,character,missing-method	isobar-analysis
estimateRatio,IBSpectra,ANY,character,character,character,NULL-method	isobar-analysis
estimateRatio,IBSpectra,ANY,character,character,missing,character-method	isobar-analysis
estimateRatio,IBSpectra,ANY,character,character,missing,data.frame-method	isobar-analysis
estimateRatio,IBSpectra,ANY,character,character,missing,matrix-method	isobar-analysis
estimateRatio,IBSpectra,ANY,character,character,NULL,character-method	isobar-analysis
estimateRatio,IBSpectra,ANY,character,character,NULL,data.frame-method	isobar-analysis
estimateRatio,IBSpectra,ANY,character,character,NULL,matrix-method	isobar-analysis
estimateRatio,IBSpectra,ANY,missing,missing,character,missing-method	isobar-analysis
estimateRatio,IBSpectra,ANY,missing,missing,missing,character-method	isobar-analysis
estimateRatioForPeptide	isobar-analysis
estimateRatioForProtein	isobar-analysis
estimateRatioNumeric	isobar-analysis
estimateRatioNumeric,numeric,numeric,missing-method	isobar-analysis
estimateRatioNumeric,numeric,numeric,NoiseModel-method	isobar-analysis
estimateRatioNumeric,numeric,numeric,NULL-method	isobar-analysis
exclude	isobar-preprocessing
exclude,IBSpectra,character-method	isobar-preprocessing
ExponentialNoANoiseModel-class	NoiseModel-class
ExponentialNoiseModel-class	NoiseModel-class
filterSpectraDeltaScore	calc.delta.score
filterSpectraPhosphoRS	getPhosphoRSProbabilities
fitCauchy	fit-distr
fitGaussianMixture	fit-distr
fitNorm	fit-distr
fitNormalCauchyMixture	fit-distr
fitTlsd	fit-distr
fitWeightedNorm	fit-distr
GeneralNoiseModel-class	NoiseModel-class
get.log	isobar-log
get.log,IBSpectra,character-method	isobar-log
get.pep.group	ProteinGroup-class
getMultUnifDensity	isobar-analysis
getMultUnifPValues	isobar-analysis
getPeptideModifContext	getPeptideModifContext
getPhosphoRSProbabilities	getPhosphoRSProbabilities
getProteinInfoFromBioDb	proteinInfo-methods
getProteinInfoFromBiomart	proteinInfo-methods
getProteinInfoFromEntrez	proteinInfo-methods
getProteinInfoFromNextProt	proteinInfo-methods
getProteinInfoFromTheInternet	proteinInfo-methods
getProteinInfoFromUniprot	proteinInfo-methods
getPtmInfoFromNextprot	getPtmInfo
getPtmInfoFromPhosphoSitePlus	getPtmInfo
get_n_proteins	isobar-reports
group-specific	specificities
groupMemberPeptides	groupMemberPeptides
GROUPSPECIFIC	specificities
human.protein.names	human.protein.names
IBSpectra	IBSpectra-class
IBSpectra-class	IBSpectra-class
ibSpectra.as.concise.data.frame	IBSpectra-class
IBSpectraTypes	IBSpectra-class
ibspiked_set1	isobar-data
ibspiked_set2	isobar-data
ib_phospho	isobar-data
indistinguishableProteins	ProteinGroup-class
indistinguishableProteins,ProteinGroup,ANY,ANY-method	ProteinGroup-class
indistinguishableProteins,ProteinGroup,character,missing-method	ProteinGroup-class
indistinguishableProteins,ProteinGroup,missing,character-method	ProteinGroup-class
indistinguishableProteins,ProteinGroup,missing,missing-method	ProteinGroup-class
indistinguishableProteins,ProteinGroup-method	ProteinGroup-class
initialize,IBSpectra-method	IBSpectra-class
initialize,NoiseModel-method	NoiseModel-class
initialize.env	isobar-reports
InverseNoANoiseModel-class	NoiseModel-class
InverseNoiseModel-class	NoiseModel-class
is.logged	isobar-log
is.logged,IBSpectra,character-method	isobar-log
isobar	isobar-package
isobar-analysis	isobar-analysis
isobar-import	isobar-import
isobar-plots	isobar-plots
isobar-preprocessing	isobar-preprocessing
isobar-reports	isobar-reports
isotopeImpurities	IBSpectra-class
isotopeImpurities,IBSpectra-method	IBSpectra-class
isotopeImpurities<-	IBSpectra-class
isotopeImpurities<-,IBSpectra-method	IBSpectra-class
iTRAQ4plexSpectra	IBSpectra-class
iTRAQ4plexSpectra-class	IBSpectra-class
iTRAQ8plexSpectra	IBSpectra-class
iTRAQ8plexSpectra-class	IBSpectra-class
iTRAQSpectra	IBSpectra-class
iTRAQSpectra-class	IBSpectra-class
load.properties	isobar-reports
load.tex.properties	isobar-reports
lowIntensity	NoiseModel-class
lowIntensity,NoiseModel-method	NoiseModel-class
lowIntensity<-	NoiseModel-class
lowIntensity<-,NoiseModel-method	NoiseModel-class
maplot	isobar-plots
maplot,IBSpectra,character,character-method	isobar-plots
maplot,IBSpectra,missing,missing-method	isobar-plots
maplot,missing,numeric,numeric-method	isobar-plots
maplot.protein	maplot.protein
maplot2	isobar-plots
maplot2,ANY,character,character-method	isobar-plots
maplot2,list,character,character-method	isobar-plots
modif.site.count	observedKnownSites
modif.sites	observedKnownSites
modifs	isobar-reports
my.protein.info	human.protein.names
n.observable.peptides	calculate.emPAI
naRegion	NoiseModel-class
naRegion,NoiseModel-method	NoiseModel-class
naRegion<-	NoiseModel-class
naRegion<-,NoiseModel-method	NoiseModel-class
noise.model.hcd	isobar-data
noiseFunction	NoiseModel-class
noiseFunction,NoiseModel-method	NoiseModel-class
NoiseModel	NoiseModel-class
NoiseModel,IBSpectra-method	NoiseModel-class
NoiseModel-class	NoiseModel-class
normalize	isobar-preprocessing
number.ranges	number.ranges
observable.peptides	calculate.emPAI
observedKnownSites	observedKnownSites
parameter	NoiseModel-class
parameter,NoiseModel-method	NoiseModel-class
parameter<-	NoiseModel-class
parameter<-,NoiseModel-method	NoiseModel-class
paste0	utils
peptide.count	peptide.count
peptideInfo	ProteinGroup-class
peptideInfo,ProteinGroup-method	ProteinGroup-class
peptideInfo-methods	ProteinGroup-class
peptideNProtein	ProteinGroup-class
peptideNProtein,ProteinGroup-method	ProteinGroup-class
peptideRatios	ratio-summ
peptideRatiosNotQuant	ratio-summ
peptides	ProteinGroup-class
peptides,ProteinGroup,character-method	ProteinGroup-class
peptides,ProteinGroup,missing-method	ProteinGroup-class
peptideSpecificity	ProteinGroup-class
peptideSpecificity,ProteinGroup-method	ProteinGroup-class
plot.NoiseModel	NoiseModel-class
plotRatio	isobar-plots
plotRatio,IBSpectra,character,character,character-method	isobar-plots
print_classlabels_tbl	isobar-reports
print_groupsize	isobar-reports
print_longtablehdr	isobar-reports
print_longtablehdr_peptide	isobar-reports
print_protein_grp_info	isobar-reports
print_protein_grp_tbl	isobar-reports
print_protein_notquant_tbl	isobar-reports
print_protein_quant_tbl	isobar-reports
print_sign_proteins_tbl	isobar-reports
property	isobar-reports
protein.ac	ProteinGroup-class
protein.ac,ProteinGroup,character-method	ProteinGroup-class
protein.ac,ProteinGroup,missing-method	ProteinGroup-class
protein.g	ProteinGroup-class
protein.g,ProteinGroup,character,character-method	ProteinGroup-class
protein.g,ProteinGroup,character-method	ProteinGroup-class
proteinDescription	proteinNameAndDescription
proteinGeneName	proteinNameAndDescription
ProteinGroup	ProteinGroup-class
proteinGroup	IBSpectra-class
ProteinGroup,data.frame,missing-method	ProteinGroup-class
ProteinGroup,data.frame,NULL-method	ProteinGroup-class
ProteinGroup,data.frame,ProteinGroup-method	ProteinGroup-class
proteinGroup,IBSpectra-method	IBSpectra-class
ProteinGroup-class	ProteinGroup-class
proteinGroup.as.concise.data.frame	ProteinGroup-class
proteinGroup<-	IBSpectra-class
proteinGroup<-,IBSpectra-method	IBSpectra-class
proteinGroupTable	ProteinGroup-class
proteinGroupTable,ProteinGroup-method	ProteinGroup-class
proteinID	proteinNameAndDescription
proteinInfo	proteinInfo-methods
proteinInfo,ProteinGroup,character,missing-method	proteinInfo-methods
proteinInfo,ProteinGroup,missing,character-method	proteinInfo-methods
proteinInfo,ProteinGroup,missing,missing-method	proteinInfo-methods
proteinInfo,ProteinGroup-method	proteinInfo-methods
proteinInfo-methods	proteinInfo-methods
proteinInfo<-	proteinInfo-methods
proteinInfo<-,ProteinGroup-method	proteinInfo-methods
proteinInfoIsOnSpliceVariants	proteinInfo-methods
proteinNameAndDescription	proteinNameAndDescription
proteinRatios	ratio-summ
protGgdata	isobar-plots
protGgdata,ANY,character,character-method	isobar-plots
raplot	isobar-plots
raplot,IBSpectra-method	isobar-plots
ratiosReshapeWide	ratiosReshapeWide
read.mzid	isobar-import
readIBSpectra	isobar-import
readIBSpectra,character,character,character-method	isobar-import
readIBSpectra,character,character,missing-method	isobar-import
readIBSpectra,character,character-method	isobar-import
readIBSpectra,character,data.frame,character-method	isobar-import
readIBSpectra,character,data.frame,missing-method	isobar-import
readPhosphoRSOutput	getPhosphoRSProbabilities
readProteinGroup	ProteinGroup-class
readProteinGroup2	ProteinGroup-class
reporter-specific	specificities
reporter.protein	reporter.protein-methods
reporter.protein,ProteinGroup,character-method	reporter.protein-methods
reporter.protein-methods	reporter.protein-methods
reporterData	IBSpectra-class
reporterData,IBSpectra-method	IBSpectra-class
reporterData<-	IBSpectra-class
reporterData<-,IBSpectra-method	IBSpectra-class
reporterIntensities	IBSpectra-class
reporterIntensities,IBSpectra-method	IBSpectra-class
reporterIntensities<-	IBSpectra-class
reporterIntensities<-,IBSpectra-method	IBSpectra-class
reporterIntensityPlot	isobar-plots
reporterIntensityPlot,IBSpectra-method	isobar-plots
reporterIntensityPlot-methods	isobar-plots
reporterMasses	IBSpectra-class
reporterMasses,IBSpectra-method	IBSpectra-class
reporterMasses<-	IBSpectra-class
reporterMasses<-,IBSpectra-method	IBSpectra-class
reporterMassPrecision	isobar-plots
reporterMassPrecision,IBSpectra,logical-method	isobar-plots
reporterMassPrecision,IBSpectra,missing-method	isobar-plots
reporterProteins	ProteinGroup-class
reporterProteins,ProteinGroup-method	ProteinGroup-class
REPORTERSPECIFIC	specificities
reporterTagMasses	IBSpectra-class
reporterTagMasses,IBSpectra-method	IBSpectra-class
reporterTagNames	IBSpectra-class
reporterTagNames,IBSpectra-method	IBSpectra-class
sanitize	sanitize
sequence.coverage	peptide.count
shared.ratios	shared.ratios
shared.ratios.sign	shared.ratios.sign
show,IBSpectra-method	IBSpectra-class
show,NoiseModel-method	NoiseModel-class
show,ProteinGroup-method	ProteinGroup-class
SPECIFICITIES	specificities
specificities	specificities
spectra.count	peptide.count
spectra.count2	spectra.count2
spectrumSel	IBSpectra-class
spectrumSel,IBSpectra,character,missing-method	IBSpectra-class
spectrumSel,IBSpectra,data.frame,missing-method	IBSpectra-class
spectrumSel,IBSpectra,matrix,missing-method	IBSpectra-class
spectrumSel,IBSpectra,missing,character-method	IBSpectra-class
spectrumSel,IBSpectra,missing,missing-method	IBSpectra-class
spectrumTitles	IBSpectra-class
spectrumTitles,IBSpectra-method	IBSpectra-class
spectrumToPeptide	ProteinGroup-class
spectrumToPeptide,ProteinGroup-method	ProteinGroup-class
stddev	NoiseModel-class
stddev,NoiseModel-method	NoiseModel-class
subsetIBSpectra	subsetIBSpectra
subtractAdditiveNoise	isobar-preprocessing
subtractAdditiveNoise,IBSpectra-method	isobar-preprocessing
summarize.ratios	ratio-summ
summary.ProteinGroup	ProteinGroup-class
tikz.proteingroup	isobar-reports
Tlsd	Tlsd-class
Tlsd-class	Tlsd-class
TlsParameter-class	TlsParameter-class
TMT10plexSpectra	IBSpectra-class
TMT10plexSpectra-class	IBSpectra-class
TMT2plexSpectra	IBSpectra-class
TMT2plexSpectra-class	IBSpectra-class
TMT6plexSpectra	IBSpectra-class
TMT6plexSpectra-class	IBSpectra-class
TMT6plexSpectra2	IBSpectra-class
TMT6plexSpectra2-class	IBSpectra-class
TMTSpectra	IBSpectra-class
TMTSpectra-class	IBSpectra-class
transform_pepmodif	isobar-reports
twodistr.plot	distr-methods
UNSPECIFIC	specificities
unspecific	specificities
variance	NoiseModel-class
variance,NoiseModel,numeric,missing-method	NoiseModel-class
variance,NoiseModel,numeric,numeric-method	NoiseModel-class
VARMETADATA	IBSpectra-class
weightedMean	ratio-summ
weightedMean,numeric,numeric-method	ratio-summ
weightedVariance	ratio-summ
weightedVariance,numeric,numeric,missing-method	ratio-summ
weightedVariance,numeric,numeric,numeric-method	ratio-summ
write.tex.commands	isobar-reports
write.xls.report	isobar-reports
writeData	IBSpectra-class
writeData,IBSpectra-method	IBSpectra-class
writeHscoreData	writeHscoreData
writeIBSpectra	writeIBSpectra
writePhosphoRSInput	getPhosphoRSProbabilities
