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 | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| human.protein.names | Info on proteins | 
| 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 | 
| load.properties | Isobar reports | 
| load.tex.properties | Isobar reports | 
| lowIntensity | NoiseModel objects | 
| lowIntensity-method | NoiseModel objects | 
| lowIntensity<- | NoiseModel objects | 
| lowIntensity<--method | NoiseModel objects | 
| 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.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 | 
| observable.peptides | emPAI approximate abundance calculations. | 
| observedKnownSites | Observed modification sites. | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| UnivariateDistribution-class | Functions for distribution calculations | 
| UNSPECIFIC | Peptide specificities | 
| unspecific | Peptide specificities | 
| variance | NoiseModel objects | 
| variance-method | NoiseModel objects | 
| VARMETADATA | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data | 
| 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 | 
| %inrange% | Isobar util functions |