Man pages for hafenr/MACode
Functions and code snippets for my master thesis
| annotateComplexFeatures | Annotate complex features using the manually annotated CORUM... |
| annotateComplexFeaturesAlt | Annotate complex features by simply checking if there is a... |
| annotateProteinTraces | Annotate protein traces with the complex id and complex name... |
| apexStringToDF | Split a list of apexes like '1,2,3,4' and create a data.frame... |
| assessComplexFeaturesWithSEC | Check for each feature in 'detected.features' if there is... |
| calcFPR | Calculate the false positive rate (== 1 - specificity) |
| calcTPR | Calculate the true positive rate (== recall) |
| calculateDetectionStatsCC | Calculate stats for the CC workflow. |
| calculateDetectionStatsPC | Calculate stats for the PC workflow. |
| computeSiteLocalizationRate | Compute for a data table of detected features how many of... |
| computeWindowedCorrelation | Compute the correlation between rows in a matrix considering... |
| convertToPCComplexFeatureFormat | Convert the output CC cprophet to a format that looks like it... |
| convertToPeptideCCData | Convert a peptide trace matrix as is input to cprophet to the... |
| corum.complex.protein.assoc | A data.table of associations between corum complexes and... |
| createCCInputData | Create input data wor the CC workflow. All this function... |
| createManualComplexAnnotations | Given a DF with columns 'complex_id', and another column... |
| deconvProteinTraces | Deconvolute a wide format data.table of protein traces using... |
| detectGroupsWithinWindow | Detect subgroups within a window. This method should be... |
| detectSubgroupsSW | Detect subgroups of proteins within a matrix of protein... |
| e4.input.proteins | A list of all proteins that are found in the traces table... |
| e4.peptide.traces.wide | A wide format data.table of peptide trace intensities. |
| e4.peptide.traces.wide.filtered | A wide format data.table of peptide trace intensities. |
| imputePartialPeakgroupCompletness | Estimate the completness of a peak group that was annotated... |
| imputeProteinConcentrations | Impute concentrations for proteins based on their total... |
| longPepTracesToWide | Convert a long list peptide trace to a wide format. export |
| longProtTracesToWide | Convert a long list protein trace to a wide format. export |
| makeROC | Make a ROC curve. |
| makeROCWithSEC | Make ROC curves and treat every SEC position as a possible... |
| makeStartParams | Create a named vector of starting parameters for an... |
| manual.annotations.full | The merged manual CORUM annotations with only those features... |
| manual.annotations.full.complete | The merged manual CORUM annotations with only those features... |
| manual.annotations.partial | The merged manual CORUM annotations with those features that... |
| manual.annotations.partial.imputed.win14.corr0.7 | Manual annotations of partial peak groups that whose... |
| manual.annotations.raw.mheusel | The raw manual complex annotations by mheusel These... |
| manual.annotations.raw.rhafen | The raw manual complex annotations by rhafen. These... |
| mergeManualComplexAnnotations | Merge the RTs for apexes of 'apex.type' for two DTs. dt1 is... |
| mergeRTs | Merge to vectors of numbers in such a way that the output... |
| nlsGaussianSum | Fit a nls model using multiple Gaussian functions. |
| nlsGaussianSumCV | Choose the best number of gaussian components automatically... |
| nlsGaussianSumCV2 | Choose the best number of gaussian components automatically... |
| plotROC | Plot the pseudo ROC curve for the output of... |
| plotSiteLocalizationRate | Plot the site localization rate for the output of... |
| plot.swResult | Plot the result of the slidingWindow algorithm. |
| plotTraces | Plot traces for a single complex or protein. |
| plotTracesWithFeaturesCC | Plot traces and features for CC wf. |
| predict.nlsGaussianSum | Predict using a nlsGaussianSum model. |
| produceProteinTraces | Sum up a list of peptide intensities into a list of protein... |
| protein.traces.2peps | Summed up protein traces using peptides from experiment 4... |
| readManualAnnotationFile | Read a TSV file where each row corresponds to an annotated... |
| removeStretchesFilter | Remove consecutive stretches from a matrix of peptide traces. |
| requireAtLeastXPeptides | Filter a list of peptide intensities s.t. only those are kept... |
| retainXMostIntensePeptides | Filter a list of peptide intensities s.t. only those peptides... |
| slidingWindowCorrelation | Compute the correlation between rows in a matrix using a... |
| widePepTracesToLong | Convert a wide format peptide trace data.table to long... |
| wideProtTracesToLong | Convert a wide format protein trace data.table to long... |
