Analysis and quantitation of isobarically tagged MSMS proteomics data


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Documentation for package ‘isobar’ version 1.4.0

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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 --

as.data.frame-method IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
as.data.frame-method ProteinGroup objects
as.data.frame.ProteinGroup ProteinGroup objects

-- C --

calculate.dNSAF dNSAF approximate abundance calculations.
calculate.emPAI emPAI approximate abundance calculations.
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 protein and peptide ratios
combn.protein.tbl protein and peptide ratios
connect.nodes Isobar reports
correctIsotopeImpurities IBSpectra preprocessing
correctIsotopeImpurities-method IBSpectra preprocessing
create.meta.reports Isobar reports
create.reports Isobar reports

-- D --

do.log Log functions for IBSpectra objects
do.log-method Log functions for IBSpectra objects
draw.boxplot Isobar reports
draw.protein.group 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 --

fitCauchy Fit weighted and unweighted Cauchy and Normal distributions
fitGaussianMixture Fit weighted and unweighted Cauchy and Normal distributions
fitGumbel 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
fitTd Fit weighted and unweighted Cauchy and Normal distributions
fitWeightedNorm Fit weighted and unweighted Cauchy and Normal distributions

-- G --

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
getProteinInfoFromBioDb Methods for Function proteinInfo
getProteinInfoFromBiomart Methods for Function proteinInfo
getProteinInfoFromNextProt Methods for Function proteinInfo
getProteinInfoFromUniprot Methods for Function proteinInfo
getPtmInfoFromNextprot Methods for Function proteinInfo
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
IBSpectraTypes IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data
ibspiked_set1 Isobar Data packages
ibspiked_set2 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
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
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.

-- P --

parameter NoiseModel objects
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.
peptideNProtein ProteinGroup objects
peptideNProtein-method ProteinGroup objects
peptideRatios protein and peptide ratios
peptides ProteinGroup objects
peptides-method ProteinGroup objects
peptideSpecificity ProteinGroup objects
peptideSpecificity-method ProteinGroup objects
plotRatio IBSpectra plots
plotRatio-method IBSpectra plots
print_longtablehdr Isobar reports
print_longtablehdr_peptide 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<- 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 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
readProteinGroup ProteinGroup objects
reporter-specific Peptide specificities
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 protein and peptide ratios
summary.ProteinGroup ProteinGroup objects

-- T --

tikz.proteingroup Isobar reports
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
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

-- U --

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 protein and peptide ratios
weightedMean-method protein and peptide ratios
weightedVariance protein and peptide ratios
weightedVariance-method protein and peptide ratios
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
writeIBSpectra Write IBSpectra file as CSV in a format readable by readIBSpectra.

-- misc --

%inrange% Isobar util functions