Analysis and quantitation of isobarically tagged MSMS proteomics
data
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Documentation for package ‘isobar’ version 1.46.0
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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 --
| 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 |