fbreitwieser/isobar
Analysis and quantitation of isobarically tagged MSMS proteomics data

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Search the fbreitwieser/isobar package
Vignettes
Functions
335
Source code
24
Man pages
44
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fbreitwieser/isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data
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API

API for fbreitwieser/isobar
Analysis and quantitation of isobarically tagged MSMS proteomics data

Global functions
%inrange% Man page
ExponentialNoANoiseModel-class Man page
ExponentialNoiseModel-class Man page
GROUPSPECIFIC Man page
GeneralNoiseModel-class Man page
IBSpectra Man page
IBSpectra-class Man page
IBSpectraTypes Man page
InverseNoANoiseModel-class Man page
InverseNoiseModel-class Man page
NoiseModel Man page
NoiseModel,IBSpectra-method Man page
NoiseModel-class Man page
ProteinGroup Man page Man page
ProteinGroup,data.frame,NULL-method Man page
ProteinGroup,data.frame,ProteinGroup-method Man page
ProteinGroup,data.frame,missing-method Man page
ProteinGroup-class Man page
REPORTERSPECIFIC Man page
SPECIFICITIES Man page
TMT10plexSpectra Man page
TMT10plexSpectra-class Man page
TMT2plexSpectra Man page
TMT2plexSpectra-class Man page
TMT6plexSpectra Man page
TMT6plexSpectra-class Man page
TMT6plexSpectra2 Man page
TMT6plexSpectra2-class Man page
TMTSpectra Man page
TMTSpectra-class Man page
TlsParameter-class Man page
Tlsd Man page
Tlsd-class Man page
UNSPECIFIC Man page
VARMETADATA Man page
adjust.ratio.pvalue Man page
as.data.frame,IBSpectra-method Man page
as.data.frame,ProteinGroup-method Man page
as.data.frame.IBSpectra Man page
as.data.frame.ProteinGroup Man page
calc.delta.score Man page
calc.pep.delta.score Man page
calcCumulativeProbXGreaterThanY Man page
calcPeptidePosition Man page
calcProbXDiffNormals Man page
calcProbXGreaterThanY Man page
calculate.dNSAF Man page
calculate.emPAI Man page
calculate.mult.sample.pvalue Man page
calculate.ratio.pvalue Man page
calculate.sample.pvalue Man page
class:IBSpectra Man page
class:NoiseModel Man page
class:ProteinGroup Man page
classLabels Man page
classLabels,IBSpectra-method Man page
classLabels<- Man page
classLabels<-,IBSpectra-method Man page
coerce,IBSpectra,data.frame-method Man page
coerce,data.frame,ProteinGroup-method Man page
combn.matrix Man page
combn.protein.tbl Man page
connect.nodes Man page
correct.peptide.ratios Man page
correctIsotopeImpurities Man page
correctIsotopeImpurities,IBSpectra-method Man page
create.meta.reports Man page
create.reports Man page
distrprint Man page
do.log Man page
do.log,IBSpectra,character-method Man page
draw.boxplot Man page
draw.protein.group Man page
draw.proteingroup.row Man page
estimateRatio Man page
estimateRatio,IBSpectra,ANY,character,character,NULL,character-m Man page
estimateRatio,IBSpectra,ANY,character,character,NULL,data.frame- Man page
estimateRatio,IBSpectra,ANY,character,character,NULL,matrix-meth Man page
estimateRatio,IBSpectra,ANY,character,character,character,NULL-m Man page
estimateRatio,IBSpectra,ANY,character,character,character,missin Man page
estimateRatio,IBSpectra,ANY,character,character,missing,characte Man page
estimateRatio,IBSpectra,ANY,character,character,missing,data.fra Man page
estimateRatio,IBSpectra,ANY,character,character,missing,matrix-m Man page
estimateRatio,IBSpectra,ANY,missing,missing,character,missing-me Man page
estimateRatio,IBSpectra,ANY,missing,missing,missing,character-me Man page
estimateRatioForPeptide Man page
estimateRatioForProtein Man page
estimateRatioNumeric Man page
estimateRatioNumeric,numeric,numeric,NULL-method Man page
estimateRatioNumeric,numeric,numeric,NoiseModel-method Man page
estimateRatioNumeric,numeric,numeric,missing-method Man page
exclude Man page
exclude,IBSpectra,character-method Man page
filterSpectraDeltaScore Man page
filterSpectraPhosphoRS Man page
fitCauchy Man page
fitGaussianMixture Man page
fitNorm Man page
fitNormalCauchyMixture Man page
fitTlsd Man page
fitWeightedNorm Man page
get.log Man page
get.log,IBSpectra,character-method Man page
get.pep.group Man page
getMultUnifDensity Man page
getMultUnifPValues Man page
getPeptideModifContext Man page
getPhosphoRSProbabilities Man page
getProteinInfoFromBioDb Man page
getProteinInfoFromBiomart Man page
getProteinInfoFromEntrez Man page
getProteinInfoFromNextProt Man page
getProteinInfoFromTheInternet Man page
getProteinInfoFromUniprot Man page
getPtmInfoFromNextprot Man page
getPtmInfoFromPhosphoSitePlus Man page
get_n_proteins Man page
group-specific Man page
groupMemberPeptides Man page
human.protein.names Man page
iTRAQ4plexSpectra Man page
iTRAQ4plexSpectra-class Man page
iTRAQ8plexSpectra Man page
iTRAQ8plexSpectra-class Man page
iTRAQSpectra Man page
iTRAQSpectra-class Man page
ibSpectra.as.concise.data.frame Man page
ib_phospho Man page
ibspiked_set1 Man page
ibspiked_set2 Man page
indistinguishableProteins Man page
indistinguishableProteins,ProteinGroup,ANY,ANY-method Man page
indistinguishableProteins,ProteinGroup,character,missing-method Man page
indistinguishableProteins,ProteinGroup,missing,character-method Man page
indistinguishableProteins,ProteinGroup,missing,missing-method Man page
indistinguishableProteins,ProteinGroup-method Man page
initialize,IBSpectra-method Man page
initialize,NoiseModel-method Man page
initialize.env Man page
is.logged Man page
is.logged,IBSpectra,character-method Man page
isobar Man page
isobar-analysis Man page
isobar-import Man page
isobar-package Man page
isobar-plots Man page
isobar-preprocessing Man page
isobar-reports Man page
isotopeImpurities Man page
isotopeImpurities,IBSpectra-method Man page
isotopeImpurities<- Man page
isotopeImpurities<-,IBSpectra-method Man page
load.properties Man page
load.tex.properties Man page
lowIntensity Man page
lowIntensity,NoiseModel-method Man page
lowIntensity<- Man page
lowIntensity<-,NoiseModel-method Man page
maplot Man page
maplot,IBSpectra,character,character-method Man page
maplot,IBSpectra,missing,missing-method Man page
maplot,missing,numeric,numeric-method Man page
maplot.protein Man page
maplot2 Man page
maplot2,ANY,character,character-method Man page
maplot2,list,character,character-method Man page
modif.site.count Man page
modif.sites Man page
modifs Man page
my.protein.info Man page
n.observable.peptides Man page
naRegion Man page
naRegion,NoiseModel-method Man page
naRegion<- Man page
naRegion<-,NoiseModel-method Man page
noise.model.hcd Man page
noiseFunction Man page
noiseFunction,NoiseModel-method Man page
normalize Man page
normalize,IBSpectra-method Man page
number.ranges Man page
observable.peptides Man page
observedKnownSites Man page
parameter Man page
parameter,NoiseModel-method Man page
parameter<- Man page
parameter<-,NoiseModel-method Man page
paste0 Man page
peptide.count Man page
peptideInfo Man page
peptideInfo,ProteinGroup-method Man page
peptideInfo-methods Man page
peptideNProtein Man page
peptideNProtein,ProteinGroup-method Man page
peptideRatios Man page
peptideRatiosNotQuant Man page
peptideSpecificity Man page Man page
peptideSpecificity,ProteinGroup-method Man page Man page
peptides Man page
peptides,ProteinGroup,character-method Man page
peptides,ProteinGroup,missing-method Man page
plot.NoiseModel Man page
plotRatio Man page
plotRatio,IBSpectra,character,character,character-method Man page
print_classlabels_tbl Man page
print_groupsize Man page
print_longtablehdr Man page
print_longtablehdr_peptide Man page
print_protein_grp_info Man page
print_protein_grp_tbl Man page
print_protein_notquant_tbl Man page
print_protein_quant_tbl Man page
print_sign_proteins_tbl Man page
property Man page
protGgdata Man page
protGgdata,ANY,character,character-method Man page
protein.ac Man page
protein.ac,ProteinGroup,character-method Man page
protein.ac,ProteinGroup,missing-method Man page
protein.g Man page
protein.g,ProteinGroup,character,character-method Man page
protein.g,ProteinGroup,character-method Man page
proteinDescription Man page
proteinGeneName Man page
proteinGroup Man page
proteinGroup,IBSpectra-method Man page
proteinGroup.as.concise.data.frame Man page
proteinGroup<- Man page
proteinGroup<-,IBSpectra-method Man page
proteinGroupTable Man page
proteinGroupTable,ProteinGroup-method Man page
proteinID Man page
proteinInfo Man page
proteinInfo,ProteinGroup,character,missing-method Man page
proteinInfo,ProteinGroup,missing,character-method Man page
proteinInfo,ProteinGroup,missing,missing-method Man page
proteinInfo,ProteinGroup-method Man page
proteinInfo-methods Man page
proteinInfo<- Man page
proteinInfo<-,ProteinGroup-method Man page
proteinInfoIsOnSpliceVariants Man page
proteinNameAndDescription Man page
proteinRatios Man page
raplot Man page
raplot,IBSpectra-method Man page
ratiosReshapeWide Man page
read.mzid Man page
readIBSpectra Man page
readIBSpectra,character,character,character-method Man page
readIBSpectra,character,character,missing-method Man page
readIBSpectra,character,character-method Man page
readIBSpectra,character,data.frame,character-method Man page
readIBSpectra,character,data.frame,missing-method Man page
readPhosphoRSOutput Man page
readProteinGroup Man page
readProteinGroup2 Man page
reporter-specific Man page
reporter.protein Man page
reporter.protein,ProteinGroup,character-method Man page
reporter.protein-methods Man page
reporterData Man page
reporterData,IBSpectra-method Man page
reporterData<- Man page
reporterData<-,IBSpectra-method Man page
reporterIntensities Man page
reporterIntensities,IBSpectra-method Man page
reporterIntensities<- Man page
reporterIntensities<-,IBSpectra-method Man page
reporterIntensityPlot Man page
reporterIntensityPlot,IBSpectra-method Man page
reporterIntensityPlot-methods Man page
reporterMassPrecision Man page
reporterMassPrecision,IBSpectra,logical-method Man page
reporterMassPrecision,IBSpectra,missing-method Man page
reporterMasses Man page
reporterMasses,IBSpectra-method Man page
reporterMasses<- Man page
reporterMasses<-,IBSpectra-method Man page
reporterProteins Man page
reporterProteins,ProteinGroup-method Man page
reporterTagMasses Man page
reporterTagMasses,IBSpectra-method Man page
reporterTagNames Man page
reporterTagNames,IBSpectra-method Man page
sanitize Man page
sequence.coverage Man page
shared.ratios Man page
shared.ratios.sign Man page
show,IBSpectra-method Man page
show,NoiseModel-method Man page
show,ProteinGroup-method Man page
specificities Man page
spectra.count Man page
spectra.count2 Man page
spectrumSel Man page
spectrumSel,IBSpectra,character,missing-method Man page
spectrumSel,IBSpectra,data.frame,missing-method Man page
spectrumSel,IBSpectra,matrix,missing-method Man page
spectrumSel,IBSpectra,missing,character-method Man page
spectrumSel,IBSpectra,missing,missing-method Man page
spectrumTitles Man page
spectrumTitles,IBSpectra-method Man page
spectrumToPeptide Man page
spectrumToPeptide,ProteinGroup-method Man page
stddev Man page
stddev,NoiseModel-method Man page
subsetIBSpectra Man page
subtractAdditiveNoise Man page
subtractAdditiveNoise,IBSpectra-method Man page
summarize.ratios Man page
summary.ProteinGroup Man page
testPdflatex Man page
testPerl Man page
tikz.proteingroup Man page
transform_pepmodif Man page
twodistr.plot Man page
unspecific Man page
variance Man page
variance,NoiseModel,numeric,missing-method Man page
variance,NoiseModel,numeric,numeric-method Man page
weightedMean Man page
weightedMean,numeric,numeric-method Man page
weightedVariance Man page
weightedVariance,numeric,numeric,missing-method Man page
weightedVariance,numeric,numeric,numeric-method Man page
write.tex.commands Man page
write.xls.report Man page
writeData Man page
writeData,IBSpectra-method Man page
writeHscoreData Man page
writeIBSpectra Man page
writePhosphoRSInput Man page
fbreitwieser/isobar documentation built on May 16, 2019, 12:01 p.m.

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