Package: isobar 1.53.0
Florian P Breitwieser
isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data
isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.
Authors:
isobar_1.53.0.tar.gz
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isobar.pdf |isobar.html✨
isobar/json (API)
NEWS
| # Install 'isobar' in R: |
| install.packages('isobar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fbreitwieser/isobar/issues
- ib_phospho - Isobar Data packages
- ibspiked_set1 - Isobar Data packages
- ibspiked_set2 - Isobar Data packages
- noise.model.hcd - Isobar Data packages
On BioConductor:isobar-1.51.0(bioc 3.20)isobar-1.50.0(bioc 3.19)
immunooncologyproteomicsmassspectrometrybioinformaticsmultiplecomparisonsqualitycontrol
Last updated 23 days agofrom:2a9239291f. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | WARNING | Oct 30 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
Exports:%inrange%adjust.ratio.pvalueas.data.frame.IBSpectraas.data.frame.ProteinGroupcalc.delta.scorecalc.pep.delta.scorecalcCumulativeProbXGreaterThanYcalcPeptidePositioncalcProbXDiffNormalscalcProbXGreaterThanYcalculate.dNSAFcalculate.emPAIcalculate.mult.sample.pvaluecalculate.ratio.pvaluecalculate.sample.pvalueclassLabelsclassLabels<-combn.matrixcombn.protein.tblconnect.nodescorrect.peptide.ratioscorrectIsotopeImpuritiescreate.meta.reportscreate.reportsdistrprintdo.logdraw.boxplotdraw.protein.groupdraw.proteingroup.rowestimateRatioestimateRatioForPeptideestimateRatioForProteinestimateRatioNumericexcludefilterSpectraDeltaScorefilterSpectraPhosphoRSfitCauchyfitGaussianMixturefitNormfitNormalCauchyMixturefitTlsdfitWeightedNormget_n_proteinsget.logget.pep.groupgetMultUnifDensitygetMultUnifPValuesgetPeptideModifContextgetPhosphoRSProbabilitiesgetProteinInfoFromBioDbgetProteinInfoFromBiomartgetProteinInfoFromEntrezgetProteinInfoFromNextProtgetProteinInfoFromTheInternetgetProteinInfoFromUniprotgetPtmInfoFromNextprotgetPtmInfoFromPhosphoSitePlusgroupMemberPeptidesGROUPSPECIFIChuman.protein.namesibSpectra.as.concise.data.frameIBSpectraTypesindistinguishableProteinsinitialize.envis.loggedisotopeImpuritiesisotopeImpurities<-load.propertiesload.tex.propertieslowIntensitylowIntensity<-maplotmaplot.proteinmodif.site.countmodif.sitesmodifsmy.protein.infon.observable.peptidesnaRegionnaRegion<-noiseFunctionNoiseModelnormalizenumber.rangesobservable.peptidesobservedKnownSitesparameterparameter<-paste0peptide.countpeptideInfopeptideNProteinpeptideRatiospeptideRatiosNotQuantpeptidespeptideSpecificityplot.NoiseModelplotRatioprint_classlabels_tblprint_groupsizeprint_longtablehdrprint_longtablehdr_peptideprint_protein_grp_infoprint_protein_grp_tblprint_protein_notquant_tblprint_protein_quant_tblprint_sign_proteins_tblpropertyprotein.acprotein.gproteinDescriptionproteinGeneNameproteinGroupProteinGroupproteinGroup.as.concise.data.frameproteinGroup<-proteinGroupTableproteinIDproteinInfoproteinInfo<-proteinInfoIsOnSpliceVariantsproteinNameAndDescriptionproteinRatiosprotGgdataraplotratiosReshapeWideread.mzidreadIBSpectrareadPhosphoRSOutputreadProteinGroupreadProteinGroup2reporter.proteinreporterDatareporterData<-reporterIntensitiesreporterIntensities<-reporterIntensityPlotreporterMassesreporterMasses<-reporterMassPrecisionreporterProteinsREPORTERSPECIFICreporterTagMassesreporterTagNamessanitizesequence.coverageshared.ratiosshared.ratios.signSPECIFICITIESspectra.countspectra.count2spectrumSelspectrumTitlesspectrumToPeptidestddevsubsetIBSpectrasubtractAdditiveNoisesummarize.ratiossummary.ProteinGrouptestPdflatextestPerltikz.proteingroupTlsdtransform_pepmodiftwodistr.plotUNSPECIFICvarianceweightedMeanweightedVariancewrite.tex.commandswrite.xls.reportwriteDatawriteHscoreDatawriteIBSpectrawritePhosphoRSInput
Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIdbplyrdigestdistrdplyrfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcpprlangRSQLiteS4VectorsscalessfsmiscstartupmsgstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrxml2XVectorzlibbioc
isobar for developers
Rendered fromisobar-devel.Rnwusingutils::Sweaveon Oct 30 2024.Last update: 2013-11-01
Started: 2013-11-01
isobar for quantification of PTM datasets
Rendered fromisobar-ptm.Rnwusingutils::Sweaveon Oct 30 2024.Last update: 2013-11-01
Started: 2013-11-01
isobar package for iTRAQ and TMT protein quantification
Rendered fromisobar.Rnwusingutils::Sweaveon Oct 30 2024.Last update: 2018-08-30
Started: 2013-11-01
Usecases for isobar package
Rendered fromisobar-usecases.Rnwusingutils::Sweaveon Oct 30 2024.Last update: 2014-11-29
Started: 2014-11-29
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analysis and quantitation of isobarically tagged MSMS proteomics data | isobar-package isobar |
| Calculate Delta Score from Ion Score | calc.delta.score calc.pep.delta.score filterSpectraDeltaScore |
| Recalculate peptide start positions based on protein sequence | calcPeptidePosition |
| Calculate and Adjust Ratio and Sample p-values. | adjust.ratio.pvalue calculate.mult.sample.pvalue calculate.ratio.pvalue calculate.sample.pvalue |
| dNSAF approximate abundance calculations. | calculate.dNSAF |
| emPAI approximate abundance calculations. | calculate.emPAI n.observable.peptides observable.peptides |
| Correct peptide ratios with protein ratios from a separate experiment. | correct.peptide.ratios |
| Functions for distribution calculations | AbscontDistribution-class calcCumulativeProbXGreaterThanY calcProbXDiffNormals calcProbXGreaterThanY Distribution-class distrprint Parameter-class twodistr.plot UnivariateDistribution-class |
| Fit weighted and unweighted Cauchy and Normal distributions | fitCauchy fitGaussianMixture fitNorm fitNormalCauchyMixture fitTlsd fitWeightedNorm |
| Get context of modification | getPeptideModifContext |
| Generate input files for PhosphoRS, call it, and get modification site probabilities | filterSpectraPhosphoRS getPhosphoRSProbabilities readPhosphoRSOutput writePhosphoRSInput |
| Get PTM site information for idenfied proteins from public databases. | getPtmInfoFromNextprot getPtmInfoFromPhosphoSitePlus |
| Peptide info for protein group members | groupMemberPeptides |
| Info on proteins | human.protein.names my.protein.info |
| IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data | as.data.frame,IBSpectra-method as.data.frame.IBSpectra class:IBSpectra classLabels classLabels,IBSpectra-method classLabels<- classLabels<-,IBSpectra-method coerce,IBSpectra,data.frame-method IBSpectra IBSpectra-class ibSpectra.as.concise.data.frame IBSpectraTypes initialize,IBSpectra-method isotopeImpurities isotopeImpurities,IBSpectra-method isotopeImpurities<- isotopeImpurities<-,IBSpectra-method iTRAQ4plexSpectra iTRAQ4plexSpectra-class iTRAQ8plexSpectra iTRAQ8plexSpectra-class iTRAQSpectra iTRAQSpectra-class proteinGroup proteinGroup,IBSpectra-method proteinGroup<- proteinGroup<-,IBSpectra-method reporterData reporterData,IBSpectra-method reporterData<- reporterData<-,IBSpectra-method reporterIntensities reporterIntensities,IBSpectra-method reporterIntensities<- reporterIntensities<-,IBSpectra-method reporterMasses reporterMasses,IBSpectra-method reporterMasses<- reporterMasses<-,IBSpectra-method reporterTagMasses reporterTagMasses,IBSpectra-method reporterTagNames reporterTagNames,IBSpectra-method show,IBSpectra-method spectrumSel spectrumSel,IBSpectra,character,missing-method spectrumSel,IBSpectra,data.frame,missing-method spectrumSel,IBSpectra,matrix,missing-method spectrumSel,IBSpectra,missing,character-method spectrumSel,IBSpectra,missing,missing-method spectrumTitles spectrumTitles,IBSpectra-method TMT10plexSpectra TMT10plexSpectra-class TMT2plexSpectra TMT2plexSpectra-class TMT6plexSpectra TMT6plexSpectra-class TMT6plexSpectra2 TMT6plexSpectra2-class TMTSpectra TMTSpectra-class VARMETADATA writeData writeData,IBSpectra-method |
| Log functions for IBSpectra objects | do.log do.log,IBSpectra,character-method get.log get.log,IBSpectra,character-method is.logged is.logged,IBSpectra,character-method |
| Isobar util functions | %inrange% paste0 |
| IBSpectra analysis: Protein and peptide ratio calculation | estimateRatio estimateRatio,IBSpectra,ANY,character,character,character,missing-method estimateRatio,IBSpectra,ANY,character,character,character,NULL-method estimateRatio,IBSpectra,ANY,character,character,missing,character-method estimateRatio,IBSpectra,ANY,character,character,missing,data.frame-method estimateRatio,IBSpectra,ANY,character,character,missing,matrix-method estimateRatio,IBSpectra,ANY,character,character,NULL,character-method estimateRatio,IBSpectra,ANY,character,character,NULL,data.frame-method estimateRatio,IBSpectra,ANY,character,character,NULL,matrix-method estimateRatio,IBSpectra,ANY,missing,missing,character,missing-method estimateRatio,IBSpectra,ANY,missing,missing,missing,character-method estimateRatioForPeptide estimateRatioForProtein estimateRatioNumeric estimateRatioNumeric,numeric,numeric,missing-method estimateRatioNumeric,numeric,numeric,NoiseModel-method estimateRatioNumeric,numeric,numeric,NULL-method getMultUnifDensity getMultUnifPValues isobar-analysis |
| Loading data into IBSpectra objects using readIBSpectra | isobar-import read.mzid readIBSpectra readIBSpectra,character,character,character-method readIBSpectra,character,character,missing-method readIBSpectra,character,character-method readIBSpectra,character,data.frame,character-method readIBSpectra,character,data.frame,missing-method |
| IBSpectra plots | isobar-plots maplot maplot,IBSpectra,character,character-method maplot,IBSpectra,missing,missing-method maplot,missing,numeric,numeric-method maplot2 maplot2,ANY,character,character-method maplot2,list,character,character-method plotRatio plotRatio,IBSpectra,character,character,character-method protGgdata protGgdata,ANY,character,character-method raplot raplot,IBSpectra-method reporterIntensityPlot reporterIntensityPlot,IBSpectra-method reporterIntensityPlot-methods reporterMassPrecision reporterMassPrecision,IBSpectra,logical-method reporterMassPrecision,IBSpectra,missing-method |
| IBSpectra preprocessing | correctIsotopeImpurities correctIsotopeImpurities,IBSpectra-method exclude exclude,IBSpectra,character-method isobar-preprocessing normalize subtractAdditiveNoise subtractAdditiveNoise,IBSpectra-method |
| Isobar reports | connect.nodes create.meta.reports create.reports draw.boxplot draw.protein.group draw.proteingroup.row get_n_proteins initialize.env isobar-reports load.properties load.tex.properties modifs print_classlabels_tbl print_groupsize print_longtablehdr print_longtablehdr_peptide print_protein_grp_info print_protein_grp_tbl print_protein_notquant_tbl print_protein_quant_tbl print_sign_proteins_tbl property testPdflatex testPerl tikz.proteingroup transform_pepmodif write.tex.commands write.xls.report |
| Isobar Data packages | ibspiked_set1 ibspiked_set2 ib_phospho noise.model.hcd |
| Ratio intensity plot for individual proteins | maplot.protein |
| NoiseModel objects | class:NoiseModel ExponentialNoANoiseModel-class ExponentialNoiseModel-class GeneralNoiseModel-class initialize,NoiseModel-method InverseNoANoiseModel-class InverseNoiseModel-class lowIntensity lowIntensity,NoiseModel-method lowIntensity<- lowIntensity<-,NoiseModel-method naRegion naRegion,NoiseModel-method naRegion<- naRegion<-,NoiseModel-method noiseFunction noiseFunction,NoiseModel-method NoiseModel NoiseModel,IBSpectra-method NoiseModel-class parameter parameter,NoiseModel-method parameter<- parameter<-,NoiseModel-method plot.NoiseModel show,NoiseModel-method stddev stddev,NoiseModel-method variance variance,NoiseModel,numeric,missing-method variance,NoiseModel,numeric,numeric-method |
| Helper function to transform number lists to ranges | number.ranges |
| Observed modification sites. | modif.site.count modif.sites observedKnownSites |
| Peptide counts, spectral counts and sequence coverage for ProteinGroup objects. | peptide.count sequence.coverage spectra.count |
| Calculating and Summarizing Protein and Peptide Ratios | combn.matrix combn.protein.tbl peptideRatios peptideRatiosNotQuant proteinRatios summarize.ratios weightedMean weightedMean,numeric,numeric-method weightedVariance weightedVariance,numeric,numeric,missing-method weightedVariance,numeric,numeric,numeric-method |
| ProteinGroup objects | as.data.frame,ProteinGroup-method as.data.frame.ProteinGroup class:ProteinGroup coerce,data.frame,ProteinGroup-method get.pep.group indistinguishableProteins indistinguishableProteins,ProteinGroup,ANY,ANY-method indistinguishableProteins,ProteinGroup,character,missing-method indistinguishableProteins,ProteinGroup,missing,character-method indistinguishableProteins,ProteinGroup,missing,missing-method indistinguishableProteins,ProteinGroup-method peptideInfo peptideInfo,ProteinGroup-method peptideInfo-methods peptideNProtein peptideNProtein,ProteinGroup-method peptides peptides,ProteinGroup,character-method peptides,ProteinGroup,missing-method peptideSpecificity peptideSpecificity,ProteinGroup-method protein.ac protein.ac,ProteinGroup,character-method protein.ac,ProteinGroup,missing-method protein.g protein.g,ProteinGroup,character,character-method protein.g,ProteinGroup,character-method ProteinGroup ProteinGroup,data.frame,missing-method ProteinGroup,data.frame,NULL-method ProteinGroup,data.frame,ProteinGroup-method ProteinGroup-class proteinGroup.as.concise.data.frame proteinGroupTable proteinGroupTable,ProteinGroup-method readProteinGroup readProteinGroup2 reporterProteins reporterProteins,ProteinGroup-method show,ProteinGroup-method spectrumToPeptide spectrumToPeptide,ProteinGroup-method summary.ProteinGroup |
| Methods for Function proteinInfo | getProteinInfoFromBioDb getProteinInfoFromBiomart getProteinInfoFromEntrez getProteinInfoFromNextProt getProteinInfoFromTheInternet getProteinInfoFromUniprot proteinInfo proteinInfo,ProteinGroup,character,missing-method proteinInfo,ProteinGroup,missing,character-method proteinInfo,ProteinGroup,missing,missing-method proteinInfo,ProteinGroup-method proteinInfo-methods proteinInfo<- proteinInfo<-,ProteinGroup-method proteinInfoIsOnSpliceVariants |
| Get protein gene names and description from protein info of protein group. | proteinDescription proteinGeneName proteinID proteinNameAndDescription |
| Reshape output of proteinRatios into wide format | ratiosReshapeWide |
| Get reporter protein group identifier for protein group identifier | reporter.protein reporter.protein,ProteinGroup,character-method reporter.protein-methods |
| Helper function for LaTeX export | sanitize |
| Shared ratio calculation | shared.ratios |
| Plot and get significantly shared ratios. | shared.ratios.sign |
| Peptide specificities | group-specific GROUPSPECIFIC reporter-specific REPORTERSPECIFIC SPECIFICITIES specificities UNSPECIFIC unspecific |
| Spectral count for peptides and proteins in ProteinGroup objects. | spectra.count2 |
| Subset IBSpectra objects | subsetIBSpectra |
| Class '"Tlsd"' | Tlsd Tlsd-class |
| Class '"TlsParameter"' | TlsParameter-class |
| Write identifications into a format suitable for Hscore. | writeHscoreData |
| Write IBSpectra file as CSV in a format readable by readIBSpectra. | writeIBSpectra |
