# Analysis and quantitation of isobarically tagged MSMS proteomics data

## Documentation for package ‘isobar’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H I L M N O P R S T U V W misc

isobar-package | Analysis and quantitation of isobarically tagged MSMS proteomics data

## -- A --

AbscontDistribution-class | Functions for distribution calculations
adjust.ratio.pvalue | Calculate and Adjust Ratio and Sample p-values.
as.data.frame-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
as.data.frame-method | ProteinGroup objects
as.data.frame.IBSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
as.data.frame.ProteinGroup | ProteinGroup objects

## -- C --

calc.delta.score | Calculate Delta Score from Ion Score
calc.pep.delta.score | Calculate Delta Score from Ion Score
calcCumulativeProbXGreaterThanY | Functions for distribution calculations
calcPeptidePosition | Recalculate peptide start positions based on protein sequence
calcProbXDiffNormals | Functions for distribution calculations
calcProbXGreaterThanY | Functions for distribution calculations
calculate.dNSAF | dNSAF approximate abundance calculations.
calculate.emPAI | emPAI approximate abundance calculations.
calculate.mult.sample.pvalue | Calculate and Adjust Ratio and Sample p-values.
calculate.ratio.pvalue | Calculate and Adjust Ratio and Sample p-values.
calculate.sample.pvalue | Calculate and Adjust Ratio and Sample p-values.
class:IBSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
class:NoiseModel | NoiseModel objects
class:ProteinGroup | ProteinGroup objects
classLabels | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
classLabels-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
classLabels<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
classLabels<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
coerce-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
coerce-method | ProteinGroup objects
combn.matrix | Calculating and Summarizing Protein and Peptide Ratios
combn.protein.tbl | Calculating and Summarizing Protein and Peptide Ratios
connect.nodes | Isobar reports
correct.peptide.ratios | Correct peptide ratios with protein ratios from a separate experiment.
correctIsotopeImpurities | IBSpectra preprocessing
correctIsotopeImpurities-method | IBSpectra preprocessing
create.meta.reports | Isobar reports
create.reports | Isobar reports

## -- D --

Distribution-class | Functions for distribution calculations
distrprint | Functions for distribution calculations
do.log | Log functions for IBSpectra objects
do.log-method | Log functions for IBSpectra objects
draw.boxplot | Isobar reports
draw.protein.group | Isobar reports
draw.proteingroup.row | Isobar reports

## -- E --

estimateRatio | IBSpectra analysis: Protein and peptide ratio calculation
estimateRatio-method | IBSpectra analysis: Protein and peptide ratio calculation
estimateRatioForPeptide | IBSpectra analysis: Protein and peptide ratio calculation
estimateRatioForProtein | IBSpectra analysis: Protein and peptide ratio calculation
estimateRatioNumeric | IBSpectra analysis: Protein and peptide ratio calculation
estimateRatioNumeric-method | IBSpectra analysis: Protein and peptide ratio calculation
exclude | IBSpectra preprocessing
exclude-method | IBSpectra preprocessing
ExponentialNoANoiseModel-class | NoiseModel objects
ExponentialNoiseModel-class | NoiseModel objects

## -- F --

filterSpectraDeltaScore | Calculate Delta Score from Ion Score
filterSpectraPhosphoRS | Generate input files for PhosphoRS, call it, and get modification site probabilities
fitCauchy | Fit weighted and unweighted Cauchy and Normal distributions
fitGaussianMixture | Fit weighted and unweighted Cauchy and Normal distributions
fitNorm | Fit weighted and unweighted Cauchy and Normal distributions
fitNormalCauchyMixture | Fit weighted and unweighted Cauchy and Normal distributions
fitTlsd | Fit weighted and unweighted Cauchy and Normal distributions
fitWeightedNorm | Fit weighted and unweighted Cauchy and Normal distributions

## -- G --

GeneralNoiseModel-class | NoiseModel objects
get.log | Log functions for IBSpectra objects
get.log-method | Log functions for IBSpectra objects
get.pep.group | ProteinGroup objects
getMultUnifDensity | IBSpectra analysis: Protein and peptide ratio calculation
getMultUnifPValues | IBSpectra analysis: Protein and peptide ratio calculation
getPeptideModifContext | Get context of modification
getPhosphoRSProbabilities | Generate input files for PhosphoRS, call it, and get modification site probabilities
getProteinInfoFromBioDb | Methods for Function proteinInfo
getProteinInfoFromBiomart | Methods for Function proteinInfo
getProteinInfoFromEntrez | Methods for Function proteinInfo
getProteinInfoFromNextProt | Methods for Function proteinInfo
getProteinInfoFromTheInternet | Methods for Function proteinInfo
getProteinInfoFromUniprot | Methods for Function proteinInfo
getPtmInfoFromNextprot | Get PTM site information for idenfied proteins from public databases.
getPtmInfoFromPhosphoSitePlus | Get PTM site information for idenfied proteins from public databases.
get_n_proteins | Isobar reports
group-specific | Peptide specificities
groupMemberPeptides | Peptide info for protein group members
GROUPSPECIFIC | Peptide specificities

## -- H --

human.protein.names | Info on proteins

## -- I --

IBSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
IBSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
ibSpectra.as.concise.data.frame | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
IBSpectraTypes | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
ibspiked_set1 | Isobar Data packages
ibspiked_set2 | Isobar Data packages
ib_phospho | Isobar Data packages
indistinguishableProteins | ProteinGroup objects
indistinguishableProteins-method | ProteinGroup objects
initialize-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
initialize-method | NoiseModel objects
initialize.env | Isobar reports
InverseNoANoiseModel-class | NoiseModel objects
InverseNoiseModel-class | NoiseModel objects
is.logged | Log functions for IBSpectra objects
is.logged-method | Log functions for IBSpectra objects
isobar | Analysis and quantitation of isobarically tagged MSMS proteomics data
isobar-analysis | IBSpectra analysis: Protein and peptide ratio calculation
isobar-import | Loading data into IBSpectra objects using readIBSpectra
isobar-plots | IBSpectra plots
isobar-preprocessing | IBSpectra preprocessing
isobar-reports | Isobar reports
isotopeImpurities | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
isotopeImpurities-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
isotopeImpurities<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
isotopeImpurities<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
iTRAQ4plexSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
iTRAQ4plexSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
iTRAQ8plexSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
iTRAQ8plexSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
iTRAQSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
iTRAQSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data

## -- L --

load.properties | Isobar reports
load.tex.properties | Isobar reports
lowIntensity | NoiseModel objects
lowIntensity-method | NoiseModel objects
lowIntensity<- | NoiseModel objects
lowIntensity<--method | NoiseModel objects

## -- M --

maplot | IBSpectra plots
maplot-method | IBSpectra plots
maplot.protein | Ratio intensity plot for individual proteins
maplot2 | IBSpectra plots
maplot2-method | IBSpectra plots
modif.site.count | Observed modification sites.
modif.sites | Observed modification sites.
modifs | Isobar reports
my.protein.info | Info on proteins

## -- N --

n.observable.peptides | emPAI approximate abundance calculations.
naRegion | NoiseModel objects
naRegion-method | NoiseModel objects
naRegion<- | NoiseModel objects
naRegion<--method | NoiseModel objects
noise.model.hcd | Isobar Data packages
noiseFunction | NoiseModel objects
noiseFunction-method | NoiseModel objects
NoiseModel | NoiseModel objects
NoiseModel-class | NoiseModel objects
NoiseModel-method | NoiseModel objects
normalize | IBSpectra preprocessing
number.ranges | Helper function to transform number lists to ranges

## -- O --

observable.peptides | emPAI approximate abundance calculations.
observedKnownSites | Observed modification sites.

## -- P --

parameter | NoiseModel objects
Parameter-class | Functions for distribution calculations
parameter-method | NoiseModel objects
parameter<- | NoiseModel objects
parameter<--method | NoiseModel objects
paste0 | Isobar util functions
peptide.count | Peptide counts, spectral counts and sequence coverage for ProteinGroup objects.
peptideInfo | ProteinGroup objects
peptideInfo-method | ProteinGroup objects
peptideInfo-methods | ProteinGroup objects
peptideNProtein | ProteinGroup objects
peptideNProtein-method | ProteinGroup objects
peptideRatios | Calculating and Summarizing Protein and Peptide Ratios
peptideRatiosNotQuant | Calculating and Summarizing Protein and Peptide Ratios
peptides | ProteinGroup objects
peptides-method | ProteinGroup objects
peptideSpecificity | ProteinGroup objects
peptideSpecificity-method | ProteinGroup objects
plot.NoiseModel | NoiseModel objects
plotRatio | IBSpectra plots
plotRatio-method | IBSpectra 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 objects
protein.ac-method | ProteinGroup objects
protein.g | ProteinGroup objects
protein.g-method | ProteinGroup objects
proteinDescription | Get protein gene names and description from protein info of protein group.
proteinGeneName | Get protein gene names and description from protein info of protein group.
ProteinGroup | ProteinGroup objects
proteinGroup | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
ProteinGroup-class | ProteinGroup objects
ProteinGroup-method | ProteinGroup objects
proteinGroup-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
proteinGroup.as.concise.data.frame | ProteinGroup objects
proteinGroup<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
proteinGroup<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
proteinGroupTable | ProteinGroup objects
proteinGroupTable-method | ProteinGroup objects
proteinID | Get protein gene names and description from protein info of protein group.
proteinInfo | Methods for Function proteinInfo
proteinInfo-method | Methods for Function proteinInfo
proteinInfo-methods | Methods for Function proteinInfo
proteinInfo<- | Methods for Function proteinInfo
proteinInfo<--method | Methods for Function proteinInfo
proteinInfoIsOnSpliceVariants | Methods for Function proteinInfo
proteinNameAndDescription | Get protein gene names and description from protein info of protein group.
proteinRatios | Calculating and Summarizing Protein and Peptide Ratios
protGgdata | IBSpectra plots
protGgdata-method | IBSpectra plots

## -- R --

raplot | IBSpectra plots
raplot-method | IBSpectra plots
ratiosReshapeWide | Reshape output of proteinRatios into wide format
read.mzid | Loading data into IBSpectra objects using readIBSpectra
readIBSpectra | Loading data into IBSpectra objects using readIBSpectra
readIBSpectra-method | Loading data into IBSpectra objects using readIBSpectra
readPhosphoRSOutput | Generate input files for PhosphoRS, call it, and get modification site probabilities
readProteinGroup | ProteinGroup objects
readProteinGroup2 | ProteinGroup objects
reporter-specific | Peptide specificities
reporter.protein | Get reporter protein group identifier for protein group identifier
reporter.protein-method | Get reporter protein group identifier for protein group identifier
reporter.protein-methods | Get reporter protein group identifier for protein group identifier
reporterData | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterData-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterData<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterData<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterIntensities | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterIntensities-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterIntensities<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterIntensities<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterIntensityPlot | IBSpectra plots
reporterIntensityPlot-method | IBSpectra plots
reporterIntensityPlot-methods | IBSpectra plots
reporterMasses | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterMasses-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterMasses<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterMasses<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterMassPrecision | IBSpectra plots
reporterMassPrecision-method | IBSpectra plots
reporterProteins | ProteinGroup objects
reporterProteins-method | ProteinGroup objects
REPORTERSPECIFIC | Peptide specificities
reporterTagMasses | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterTagMasses-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterTagNames | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
reporterTagNames-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data

## -- S --

sanitize | Helper function for LaTeX export
sequence.coverage | Peptide counts, spectral counts and sequence coverage for ProteinGroup objects.
shared.ratios | Shared ratio calculation
shared.ratios.sign | Plot and get significantly shared ratios.
show-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
show-method | NoiseModel objects
show-method | ProteinGroup objects
SPECIFICITIES | Peptide specificities
specificities | Peptide specificities
spectra.count | Peptide counts, spectral counts and sequence coverage for ProteinGroup objects.
spectra.count2 | Spectral count for peptides and proteins in ProteinGroup objects.
spectrumSel | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
spectrumSel-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
spectrumTitles | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
spectrumTitles-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
spectrumToPeptide | ProteinGroup objects
spectrumToPeptide-method | ProteinGroup objects
stddev | NoiseModel objects
stddev-method | NoiseModel objects
subsetIBSpectra | Subset IBSpectra objects
subtractAdditiveNoise | IBSpectra preprocessing
subtractAdditiveNoise-method | IBSpectra preprocessing
summarize.ratios | Calculating and Summarizing Protein and Peptide Ratios
summary.ProteinGroup | ProteinGroup objects

## -- T --

testPdflatex | Isobar reports
testPerl | Isobar reports
tikz.proteingroup | Isobar reports
Tlsd | Class '"Tlsd"'
Tlsd-class | Class '"Tlsd"'
TlsParameter-class | Class '"TlsParameter"'
TMT10plexSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
TMT10plexSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
TMT2plexSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
TMT2plexSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
TMT6plexSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
TMT6plexSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
TMT6plexSpectra2 | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
TMT6plexSpectra2-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
TMTSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
TMTSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
transform_pepmodif | Isobar reports
twodistr.plot | Functions for distribution calculations

## -- U --

UnivariateDistribution-class | Functions for distribution calculations
UNSPECIFIC | Peptide specificities
unspecific | Peptide specificities

## -- V --

variance | NoiseModel objects
variance-method | NoiseModel objects
VARMETADATA | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data

## -- W --

weightedMean | Calculating and Summarizing Protein and Peptide Ratios
weightedMean-method | Calculating and Summarizing Protein and Peptide Ratios
weightedVariance | Calculating and Summarizing Protein and Peptide Ratios
weightedVariance-method | Calculating and Summarizing Protein and Peptide Ratios
write.tex.commands | Isobar reports
write.xls.report | Isobar reports
writeData | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
writeData-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
writeHscoreData | Write identifications into a format suitable for Hscore.
writeIBSpectra | Write IBSpectra file as CSV in a format readable by readIBSpectra.
writePhosphoRSInput | Generate input files for PhosphoRS, call it, and get modification site probabilities

## -- misc --

%inrange% | Isobar util functions