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

Global functions
%inrange% Man page
AbscontDistribution-class Man page
Distribution-class Man page
ExponentialNoANoiseModel-class Man page
ExponentialNoiseModel-class Man page
GeneralNoiseModel-class Man page
IBSpectra Man page
IBSpectra-class Man page
IBSpectraAsConciseDataFrameNew Source code
IBSpectraTypes Man page Source code
InverseNoANoiseModel-class Man page
InverseNoiseModel-class Man page
NULLstring Source code
NoiseModel Man page
NoiseModel,IBSpectra-method Man page
NoiseModel-class Man page
Parameter-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
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 Source code
Tlsd-class Man page
UnivariateDistribution-class Man page
abbrev Source code
add.quant.to.xls.tbl Source code
adjust.ratio.pvalue Man page Source code
all.duplicate.rows Source code
all.duplicates Source code
as.data.frame,IBSpectra-method Man page
as.data.frame,ProteinGroup-method Man page
as.data.frame.IBSpectra Man page Source code
as.data.frame.ProteinGroup Man page Source code
as.matrix Source code
as.vect Source code
bnds Source code Source code
build.protein.group Source code
calc.col Source code
calc.delta.score Man page Source code
calc.lm Source code
calc.pep.delta.score Man page Source code
calc.seqcov Source code
calc.weighted.lm Source code
calc.weighted.ratio Source code
calc.zscore Source code Source code
calcCumulativeProbXGreaterThanY Man page Source code
calcPeptidePosition Man page Source code
calcProbXDiffNormals Man page Source code
calcProbXGreaterThanY Man page Source code
calcProbXGreaterThanY.orig Source code
calculate.dNSAF Man page Source code
calculate.emPAI Man page Source code
calculate.mult.sample.pvalue Man page Source code
calculate.mw Source code
calculate.ratio.pvalue Man page Source code
calculate.sample.pvalue Man page Source code
call.cmd Source code
call.estimateRatio Source code
check.assayDataElements Source code
check.columns Source code
check.isfunction Source code
check.property Source code
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
cn Source code
coerce,IBSpectra,data.frame-method Man page
coerce,data.frame,ProteinGroup-method Man page
combine.fisher Source code
combine.fisher.tblwide Source code
combn.matrix Man page Source code
combn.protein.tbl Man page Source code
compile.tex Source code
concensus.il.peptide Source code
connect.nodes Man page Source code
consolidate.charge Source code
consolidate.modification.pos Source code
consolidate.peptide.ids Source code
convert.msgfp.pepmodif Source code
convert.msgfp.protein Source code
convertModifToPhosphoRS Source code
convertModifToPos Source code
convertPeptideModif Source code
convertPhosphoRSPepProb Source code
correct.peptide.ratios Man page Source code
correctIsotopeImpurities Man page
correctIsotopeImpurities,IBSpectra-method Man page
create.meta.reports Man page Source code
create.or.load Source code
create.or.load.ibspectra Source code
create.or.load.merged.table Source code
create.or.load.my.protein.infos Source code
create.or.load.noise.model Source code
create.or.load.ptm.info Source code
create.or.load.quant.table Source code
create.or.load.ratiodistr Source code
create.or.load.ratiodistr.ratios Source code
create.or.load.xls.quant.tbl Source code
create.reports Man page Source code
create.xls.peptide.quant.tbl Source code
create.xls.protein.quant.tbl Source code
dissect.search.engines Source code
distrprint Man page Source code
do.create.protein.info Source code
do.log Man page
do.log,IBSpectra,character-method Man page
do.map Source code
do.resolve.conflicts Source code
draw.boxplot Man page Source code
draw.protein.group Man page Source code
draw.proteingroup.row Man page Source code
env.copy Source code
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 Source code
estimateRatioForProtein Man page Source code
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
exists.property Source code
expand.w.vector Source code
extend.protein.group Source code
factor.as.character Source code
factor.to.chr Source code
filterSpectraDeltaScore Man page Source code
filterSpectraPhosphoRS Man page Source code
fitCauchy Man page Source code
fitGaussianMixture Man page Source code
fitNorm Man page Source code
fitNormalCauchyMixture Man page Source code
fitTlsd Man page Source code
fitWeightedNorm Man page Source code
fix.il.peptide Source code
get.cmbn Source code
get.cols Source code
get.database Source code
get.dupl.n.warn Source code
get.log Man page
get.log,IBSpectra,character-method Man page
get.merged.table Source code
get.modif.pos Source code
get.modif.pos.for.ac Source code
get.names Source code
get.normalization.factors Source code
get.or.load Source code
get.pep.group Man page Source code
get.property Source code
get.quant Source code
get.quant.elems Source code
get.ri Source code Source code
get.tbl.pg Source code
get.varMetaData Source code
getModifOnPosition Source code
getMultUnifDensity Man page Source code
getMultUnifPValues Man page Source code
getPeptideModifContext Man page Source code
getPhosphoRSProbabilities Man page Source code
getProteinInfoFromBioDb Man page Source code
getProteinInfoFromBiomart Man page Source code
getProteinInfoFromEntrez Man page Source code
getProteinInfoFromNextProt Man page Source code
getProteinInfoFromTheInternet Man page Source code
getProteinInfoFromUniprot Man page Source code
getPtmInfoFromNextprot Man page Source code
getPtmInfoFromPhosphoSitePlus Man page Source code
get_n_proteins Man page Source code
gg_element_text Source code
gg_theme Source code
grep_columns Source code
group-specific Man page
groupMemberPeptides Man page Source code
has.modif Source code
human.protein.names Man page Source code
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 Source code
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 Source code
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
lines.nf Source code
lines.nm Source code
load.properties Man page Source code
load.property Source code
load.tex.properties Man page Source code
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 Source code
maplot2 Man page
maplot2,ANY,character,character-method Man page
maplot2,list,character,character-method Man page
max.uniq Source code
mean.na.rm Source code
merge.identifications Source code
merge.identifications.full Source code
merge.quant.identifications Source code
merge.search.engine.identifications Source code
modif.site.count Man page Source code
modif.sites Man page Source code
modifs Man page
most Source code
moveToFirstCol Source code
my.protein.info Man page Source code
n.observable.peptides Man page Source code
na.rm Source code
naRegion Man page
naRegion,NoiseModel-method Man page
naRegion<- Man page
naRegion<-,NoiseModel-method Man page
names.as.vector Source code
noise.model.hcd Man page
noiseFunction Man page
noiseFunction,NoiseModel-method Man page
normalize Man page Source code
normalize,IBSpectra-method Man page
number.ranges Man page Source code
observable.peptides Man page Source code
observedKnownSites Man page Source code
onAttach Source code
panel.cor Source code
panel.smooth Source code
panel.txt Source code
parameter Man page
parameter,NoiseModel-method Man page
parameter<- Man page
parameter<-,NoiseModel-method Man page
paste0 Man page Source code
paste_unique Source code
peptide.count Man page Source code
peptideInfo Man page
peptideInfo,ProteinGroup-method Man page
peptideInfo-methods Man page
peptideNProtein Man page
peptideNProtein,ProteinGroup-method Man page
peptideRatios Man page Source code
peptideRatiosNotQuant Man page Source code
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 Source code
plot.data Source code
plot.heatmaps Source code
plot.heatmaps.gd Source code
plot.pairs Source code
plotRatio Man page
plotRatio,IBSpectra,character,character,character-method Man page
print.proteinrow Source code
print_classlabels_tbl Man page Source code
print_groupsize Man page Source code
print_longtablehdr Man page Source code
print_longtablehdr_peptide Man page Source code
print_protein_grp_info Man page Source code
print_protein_grp_tbl Man page Source code
print_protein_notquant_tbl Man page Source code
print_protein_quant_tbl Man page Source code
print_sign_proteins_tbl Man page Source code
property Man page Source code
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.acc Source code
protein.g Man page
protein.g,ProteinGroup,character,character-method Man page
protein.g,ProteinGroup,character-method Man page
proteinDescription Man page Source code
proteinGeneName Man page Source code
proteinGroup Man page
proteinGroup,IBSpectra-method Man page
proteinGroup.as.concise.data.frame Man page Source code
proteinGroup<- Man page
proteinGroup<-,IBSpectra-method Man page
proteinGroupAsConciseDataFrame Source code
proteinGroupAsConciseDataFrame1 Source code
proteinGroupTable Man page
proteinGroupTable,ProteinGroup-method Man page
proteinID Man page Source code
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.ok Source code
proteinInfo<- Man page
proteinInfo<-,ProteinGroup-method Man page
proteinInfoIsOnSpliceVariants Man page Source code
proteinNameAndDescription Man page Source code
proteinPtmInfo Source code
proteinRatios Man page Source code
proteins.w.shared.peptides Source code
raplot Man page
raplot,IBSpectra-method Man page
ratiosReshapeWide Man page Source code
read.identifications Source code
read.idfile Source code
read.idfile.df Source code
read.mgf Source code
read.msgfp.tsv Source code
read.mzid Man page Source code
read.peaklist Source code
read.rockerbox Source code
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 Source code
readProteinGroup Man page Source code
readProteinGroup2 Man page Source code
remove.duplications Source code
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
reshapeLong Source code
resolve.conflicts Source code
resolve.differing.identifications Source code
resolve.modifications Source code
return.equal.or.na Source code
round.distr Source code
sanitize Man page Source code
sanitize.sh Source code
scatter.plot Source code
searchengine.cols Source code
sel.outliers Source code
sequence.coverage Man page Source code
set Source code
shared.ratios Man page Source code
shared.ratios.sign Man page Source code
show,IBSpectra-method Man page
show,NoiseModel-method Man page
show,ProteinGroup-method Man page
simplify.seqcov Source code
specificities Man page
spectra.count Man page Source code
spectra.count2 Man page Source code
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
stopiflengthnotequal Source code
stopifna Source code
stopifnot Source code
string.number.ranges Source code
strsplit_vector Source code
subsetIBSpectra Man page Source code
subtractAdditiveNoise Man page
subtractAdditiveNoise,IBSpectra-method Man page
sum.bool Source code
sum.bool.c Source code
sum.bool.na Source code
summarize.pepmodif Source code
summarize.ratios Man page Source code
summarize.splice.variants Source code
summary.ProteinGroup Man page Source code
take.max Source code
testPdflatex Man page Source code
testPerl Man page Source code
tex.combinenames Source code
tikz.proteingroup Man page Source code
transform_pepmodif Man page Source code
trim Source code
ttest.pval Source code
ttest.pval.se Source code
twodistr.plot Man page Source code
unique.or.collapse Source code
unspecific Man page
valid.IBSpectra Source code
valid.IBSpectra.slots Source code
valid.NoiseModel Source code
valid.NoiseModel.slots Source code
valid.ProteinGroup Source code
valid.ProteinGroup.slots Source code
variance Man page
variance,NoiseModel,numeric,missing-method Man page
variance,NoiseModel,numeric,numeric-method Man page
vector.as.data.frame Source code
weighted.cor Source code
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.summarized.table Source code
write.t Source code
write.tex.commands Man page Source code
write.xls.report Man page Source code Source code
writeData Man page Source code
writeData,IBSpectra-method Man page
writeHscoreData Man page Source code
writeIBSpectra Man page Source code
writePhosphoRSInput Man page Source code
isobar documentation built on Nov. 1, 2018, 2:10 a.m.