Man pages for hafenr/MACode
Functions and code snippets for my master thesis

annotateComplexFeaturesAnnotate complex features using the manually annotated CORUM...
annotateComplexFeaturesAltAnnotate complex features by simply checking if there is a...
annotateProteinTracesAnnotate protein traces with the complex id and complex name...
apexStringToDFSplit a list of apexes like '1,2,3,4' and create a data.frame...
assessComplexFeaturesWithSECCheck for each feature in 'detected.features' if there is...
calcFPRCalculate the false positive rate (== 1 - specificity)
calcTPRCalculate the true positive rate (== recall)
calculateDetectionStatsCCCalculate stats for the CC workflow.
calculateDetectionStatsPCCalculate stats for the PC workflow.
computeSiteLocalizationRateCompute for a data table of detected features how many of...
computeWindowedCorrelationCompute the correlation between rows in a matrix considering...
convertToPCComplexFeatureFormatConvert the output CC cprophet to a format that looks like it...
convertToPeptideCCDataConvert a peptide trace matrix as is input to cprophet to the...
corum.complex.protein.assocA data.table of associations between corum complexes and...
createCCInputDataCreate input data wor the CC workflow. All this function...
createManualComplexAnnotationsGiven a DF with columns 'complex_id', and another column...
deconvProteinTracesDeconvolute a wide format data.table of protein traces using...
detectGroupsWithinWindowDetect subgroups within a window. This method should be...
detectSubgroupsSWDetect subgroups of proteins within a matrix of protein...
e4.input.proteinsA list of all proteins that are found in the traces table...
e4.peptide.traces.wideA wide format data.table of peptide trace intensities.
e4.peptide.traces.wide.filteredA wide format data.table of peptide trace intensities.
imputePartialPeakgroupCompletnessEstimate the completness of a peak group that was annotated...
imputeProteinConcentrationsImpute concentrations for proteins based on their total...
longPepTracesToWideConvert a long list peptide trace to a wide format. export
longProtTracesToWideConvert a long list protein trace to a wide format. export
makeROCMake a ROC curve.
makeROCWithSECMake ROC curves and treat every SEC position as a possible...
makeStartParamsCreate a named vector of starting parameters for an...
manual.annotations.fullThe merged manual CORUM annotations with only those features...
manual.annotations.full.completeThe merged manual CORUM annotations with only those features...
manual.annotations.partialThe merged manual CORUM annotations with those features that...
manual.annotations.partial.imputed.win14.corr0.7Manual annotations of partial peak groups that whose...
manual.annotations.raw.mheuselThe raw manual complex annotations by mheusel These...
manual.annotations.raw.rhafenThe raw manual complex annotations by rhafen. These...
mergeManualComplexAnnotationsMerge the RTs for apexes of 'apex.type' for two DTs. dt1 is...
mergeRTsMerge to vectors of numbers in such a way that the output...
nlsGaussianSumFit a nls model using multiple Gaussian functions.
nlsGaussianSumCVChoose the best number of gaussian components automatically...
nlsGaussianSumCV2Choose the best number of gaussian components automatically...
plotROCPlot the pseudo ROC curve for the output of...
plotSiteLocalizationRatePlot the site localization rate for the output of...
plot.swResultPlot the result of the slidingWindow algorithm.
plotTracesPlot traces for a single complex or protein.
plotTracesWithFeaturesCCPlot traces and features for CC wf.
predict.nlsGaussianSumPredict using a nlsGaussianSum model.
produceProteinTracesSum up a list of peptide intensities into a list of protein...
protein.traces.2pepsSummed up protein traces using peptides from experiment 4...
readManualAnnotationFileRead a TSV file where each row corresponds to an annotated...
removeStretchesFilterRemove consecutive stretches from a matrix of peptide traces.
requireAtLeastXPeptidesFilter a list of peptide intensities s.t. only those are kept...
retainXMostIntensePeptidesFilter a list of peptide intensities s.t. only those peptides...
slidingWindowCorrelationCompute the correlation between rows in a matrix using a...
widePepTracesToLongConvert a wide format peptide trace data.table to long...
wideProtTracesToLongConvert a wide format protein trace data.table to long...
hafenr/MACode documentation built on May 14, 2017, 10:20 p.m.