Files in ludgergoeminne/MSqRob

Robust statistical inference for quantitative LC-MS proteomics

CHANGELOG.md R/MSnSet2protdata.R R/addFactorInterations.R R/addVarFromVar.R R/countPeptides.R R/df2protdata.R R/dummyVars_MSqRob.R R/fdrtool_subset.R R/fit_model.R R/getBetaVcovDf.R R/getBetaVcovDfList.R R/makeContrast.R R/preprocess_MaxQuant.R R/preprocess_hlpFunctions.R R/preprocess_long.R R/preprocess_wide.R R/protLM.R R/prot_p_adjust.R R/prot_p_adjust_protwise.R R/prot_signif.R R/protdata.R R/saves_loads_MSqRob.R R/sechol.R R/sigma.R R/smallestUniqueGroups.R R/squeezePars.R R/squeezeVarRob.R R/testANOVA.R R/testContrast.R R/testProtLMContrast.R R/test_contrast_adjust.R R/test_contrast_stagewise.R R/updateProgress.R README.md inst/App-MSqRob/UI.R inst/App-MSqRob/directoryInput.R inst/App-MSqRob/downloadHandler.R inst/App-MSqRob/global.R inst/App-MSqRob/server.R inst/App-MSqRob/utilities.R inst/App-MSqRob/www/UI.R inst/App-MSqRob/www/directoryInput.R inst/App-MSqRob/www/global.R inst/App-MSqRob/www/server.R man/MSnSet2protdata.Rd man/addFactorInteractions.Rd man/addVarFromVar.Rd man/adjustNames.Rd man/countPeptides.Rd man/cutOffPval.Rd man/df2protdata.Rd man/dummyVars_MSqRob.Rd man/fdrtool_subset.Rd man/fit.model.Rd man/getAccessions-protLM-method.Rd man/getAccessions-protdata-method.Rd man/getAnnotations-protLM-method.Rd man/getAnnotations-protdata-method.Rd man/getBetaVcovDf-glm-method.Rd man/getBetaVcovDf-glmerMod-method.Rd man/getBetaVcovDf-lm-method.Rd man/getBetaVcovDf-lmerMod-method.Rd man/getBetaVcovDfList.Rd man/getData-protdata-method.Rd man/getModels-protLM-method.Rd man/getPData-protdata-method.Rd man/getThetaVars.Rd man/get_qvals.Rd man/import2MSnSet.Rd man/importDIAData.Rd man/index2Numeric.Rd man/init_ann_MQ_Excel.Rd man/inspect_loads_MSqRob.Rd man/length-protLM-method.Rd man/length-protdata-method.Rd man/loads_MSqRob.Rd man/makeAnnotation.Rd man/makeContrast.Rd man/pasteAnnotation.Rd man/plot_fdrtool.Rd man/preprocess_MSnSet.Rd man/preprocess_MaxQuant.Rd man/preprocess_generic.Rd man/preprocess_long.Rd man/preprocess_wide.Rd man/prot.p.adjust.Rd man/prot.p.adjust_protwise.Rd man/prot.signif.Rd man/protLM-class.Rd man/protdata-class.Rd man/read2MSnSet.Rd man/read_MaxQuant.Rd man/read_moFF.Rd man/saves_MSqRob.Rd man/selectAccessions-protdata-method.Rd man/setAccessions-protLM-method.Rd man/setAccessions-protdata-method.Rd man/setAnnotations-protLM-method.Rd man/setAnnotations-protdata-method.Rd man/setData-protdata-method.Rd man/setModels-protLM-method.Rd man/smallestUniqueGroups.Rd man/squeezePars.Rd man/squeezeThetas.Rd man/squeezeVarRob.Rd man/sub-protLM-ANY-ANY-ANY-method.Rd man/sub-protdata-ANY-ANY-ANY-method.Rd man/test.ANOVA.Rd man/test.contrast.Rd man/test.contrast_adjust.Rd man/test.contrast_stagewise.Rd man/test.protLMcontrast.Rd man/update.lmerMod.Rd man/update_protLM.Rd vignettes/MSqRob.Rmd vignettes/plotfunctions.R