API for ludgergoeminne/MSqRob
Robust statistical inference for quantitative LC-MS proteomics
| Global functions | |
|---|---|
| .ProtLM.print | Source code |
| .Protdata.print | Source code |
| .checkPredictors | Source code |
| .createLmList | Source code |
| .createParsedFormula | Source code |
| .createRidgeList | Source code |
| .emptyLM | Source code |
| .emptylmerMod | Source code |
| .errorCheckFit | Source code |
| .getBetaVcovDfLm | Source code |
| .getBetaVcovDfMermod | Source code |
| .getDfLm | Source code |
| .getDfMermod | Source code |
| .getMoreLevels | Source code |
| .getSigmaLm | Source code |
| .getSigmaMermod | Source code |
| .lmEstM3 | Source code |
| .makeFormulaPredictors | Source code |
| .normaliseMSnSet | Source code |
| .normalizeRLR | Source code |
| .protLM.valid | Source code |
| .protdata.valid | Source code |
| .removeSingleLevels | Source code |
| .replaceFixed | Source code |
| .ridgeEstM3 | Source code |
| .squeezeVarRob | Source code |
| .weightsLmFit | Source code |
| MSnSet2protdata | Man page Source code |
| [,protLM,ANY,ANY,ANY-method | Man page |
| [,protdata,ANY,ANY,ANY-method | Man page |
| addColClasses | Source code |
| addFactorInteractions | Man page Source code |
| addVarFromVar | Man page Source code |
| addZerosQR | Source code |
| adjustNames | Man page Source code |
| adjust_stage2 | Source code |
| aggregateMSnSet | Source code |
| calculate_qvals | Source code |
| check_expAnn | Source code |
| contr.ltfr_MSqRob | Man page Man page |
| countPeptides | Man page Source code |
| cutOffPval | Man page Source code |
| devFun | Source code |
| devianceForHessian | Source code |
| df2protdata | Man page Source code |
| dfBetweenWithin | Source code |
| dfSatterthwaite | Source code |
| dummyVars_MSqRob | Man page |
| dummyVars_MSqRob.default | Man page Man page |
| fdrtool_subset | Man page |
| fit.model | Man page Source code |
| fitFDistRobustly_LG | Source code |
| fitFDist_LG | Source code |
| getAccessions,protLM-method | Man page |
| getAccessions,protdata-method | Man page |
| getAnnotationRun | Source code |
| getAnnotations,protLM-method | Man page |
| getAnnotations,protdata-method | Man page |
| getBetaVcovDf,glm-method | Man page |
| getBetaVcovDf,glmerMod-method | Man page |
| getBetaVcovDf,lm-method | Man page |
| getBetaVcovDf,lmerMod-method | Man page |
| getBetaVcovDfList | Man page Source code |
| getComp_preds | Source code |
| getData,protdata-method | Man page |
| getModels,protLM-method | Man page |
| getN | Source code |
| getPData,protdata-method | Man page |
| getPartSet | Source code |
| getPs | Source code |
| getThetaVars | Man page Source code |
| getVcovBetaBforGrad | Source code |
| getXlevels | Source code |
| get_qvals | Man page Source code |
| import2MSnSet | Man page Source code |
| importDIAData | Man page |
| index2Numeric | Man page Source code |
| init_ann_Excel | Source code |
| init_ann_MQ_Excel | Man page |
| inspect_loads_MSqRob | Man page |
| length,protLM-method | Man page |
| length,protdata-method | Man page |
| loads_MSqRob | Man page |
| makeAnnotation | Man page Source code |
| makeContrast | Man page Source code |
| makeContrastMatrix | Source code |
| make_pData_MSqRob | Source code |
| pasteAnnotation | Man page Source code |
| plot_fdrtool | Man page Source code |
| predict.dummyVars_MSqRob | Man page Man page Source code |
| preprocess_MSnSet | Man page Source code |
| preprocess_MaxQuant | Man page Source code |
| preprocess_generic | Man page Source code |
| preprocess_long | Man page Source code |
| preprocess_wide | Man page Source code |
| print.protLM | Source code |
| print.protdata | Source code |
| prot.p.adjust | Man page Source code |
| prot.p.adjust_protwise | Man page Source code |
| prot.signif | Man page Source code |
| protLM-class | Man page |
| protdata-class | Man page |
| read2MSnSet | Man page |
| read_MaxQuant | Man page Source code |
| read_moFF | Man page Source code |
| saves_MSqRob | Man page |
| sechol | Source code |
| selectAccessions,protdata-method | Man page |
| setAccessions,protLM-method | Man page |
| setAccessions,protdata-method | Man page |
| setAnnotations,protLM-method | Man page |
| setAnnotations,protdata-method | Man page |
| setData,protdata-method | Man page |
| setModels,protLM-method | Man page |
| smallestUniqueGroups | Man page Source code |
| squeezePars | Man page Source code |
| squeezeThetas | Man page Source code |
| squeezeVarRob | Man page Source code |
| test.ANOVA | Man page Source code |
| test.contrast | Man page Source code |
| test.contrast_adjust | Man page Source code |
| test.contrast_stagewise | Man page Source code |
| test.protLMcontrast | Man page Source code |
| update.lmerMod | Man page Source code |
| updateProgress | Source code |
| update_protLM | Man page Source code |
