Files in hafenr/MACode
Functions and code snippets for my master thesis
.Rbuildignore
.gitignore
DESCRIPTION
MACode.Rproj
NAMESPACE
R/LDAscoring.R
R/RcppExports.R
R/benchmarkAnalysisCC.R
R/benchmarkAnalysisPC.R
R/complexCentricWorkflow.R
R/data.R
R/dataConversion.R
R/dataImputation.R
R/dataVisualization.R
R/imputePartialPeakgroupCompleteness.R
R/manualComplexFeatureAnnotation.R
R/nlsGaussianSum.R
R/peptideFilters.R
R/slidingWindowCorrelation.R
R/slidingWindowSubgroupDetection.R
README.md
data-raw/HEK293_protein_conc_estimates.R
data-raw/HEK293_protein_conc_estimates.csv
data-raw/corum.complex.protein.assoc.R
data-raw/corum_complex_protein_assoc.tsv
data/HEK293.protein.conc.estimates.rda
data/corum.complex.protein.assoc.rda
data/e4.input.proteins.rda
data/e4.peptide.traces.wide.filtered.rda
data/e4.peptide.traces.wide.rda
data/features.deconv.rda
data/manual.annotations.final.rda
data/manual.annotations.full.complete.rda
data/manual.annotations.full.rda
data/manual.annotations.partial.imputed.win14.corr0.7.rda
data/manual.annotations.partial.rda
data/manual.annotations.raw.mheusel.rda
data/manual.annotations.raw.rhafen.rda
data/peptide_traces_matrix.tsv
data/protein.traces.2peps.rda
data/protein.traces.2peps.with.complex.rda
data/stats.pc.final.rda
man/annotateComplexFeatures.Rd
man/annotateComplexFeaturesAlt.Rd
man/annotateProteinTraces.Rd
man/apexStringToDF.Rd
man/assessComplexFeaturesWithSEC.Rd
man/calcFPR.Rd
man/calcTPR.Rd
man/calculateDetectionStatsCC.Rd
man/calculateDetectionStatsPC.Rd
man/computeSiteLocalizationRate.Rd
man/computeWindowedCorrelation.Rd
man/convertToPCComplexFeatureFormat.Rd
man/convertToPeptideCCData.Rd
man/corum.complex.protein.assoc.Rd
man/createCCInputData.Rd
man/createManualComplexAnnotations.Rd
man/deconvProteinTraces.Rd
man/detectGroupsWithinWindow.Rd
man/detectSubgroupsSW.Rd
man/e4.input.proteins.Rd
man/e4.peptide.traces.wide.Rd
man/e4.peptide.traces.wide.filtered.Rd
man/imputePartialPeakgroupCompletness.Rd
man/imputeProteinConcentrations.Rd
man/longPepTracesToWide.Rd
man/longProtTracesToWide.Rd
man/makeROC.Rd
man/makeROCWithSEC.Rd
man/makeStartParams.Rd
man/manual.annotations.full.Rd
man/manual.annotations.full.complete.Rd
man/manual.annotations.partial.Rd
man/manual.annotations.partial.imputed.win14.corr0.7.Rd
man/manual.annotations.raw.mheusel.Rd
man/manual.annotations.raw.rhafen.Rd
man/mergeManualComplexAnnotations.Rd
man/mergeRTs.Rd
man/nlsGaussianSum.Rd
man/nlsGaussianSumCV.Rd
man/nlsGaussianSumCV2.Rd
man/plot.swResult.Rd
man/plotROC.Rd
man/plotSiteLocalizationRate.Rd
man/plotTraces.Rd
man/plotTracesWithFeaturesCC.Rd
man/predict.nlsGaussianSum.Rd
man/produceProteinTraces.Rd
man/protein.traces.2peps.Rd
man/readManualAnnotationFile.Rd
man/removeStretchesFilter.Rd
man/requireAtLeastXPeptides.Rd
man/retainXMostIntensePeptides.Rd
man/slidingWindowCorrelation.Rd
man/widePepTracesToLong.Rd
man/wideProtTracesToLong.Rd
src/.gitignore
src/RcppExports.cpp
src/removeStretchesFilter.cpp
