Man pages for wrProteo
Proteomics Data Analysis Functions
| AAmass | Molecular mass for amino-acids |
| AucROC | AUC from ROC-curves |
| cleanListCoNames | Selective batch cleaning of sample- (ie column-) names in... |
| combineMultFilterNAimput | Combine Multiple Filters On NA-imputed Data |
| convAASeq2mass | Molecular mass for amino-acids |
| corColumnOrder | Order Columns In List Of Matrixes, Data.frames And Vectors |
| countNoOfCommonPeptides | Compare in-silico digested proteomes for unique and shared... |
| dot-atomicMasses | Molecular mass for Elements |
| dot-checkKnitrProt | Checking presence of knitr and rmarkdown |
| dot-checkSetupGroups | Additional/final Check And Adjustments To Sample-order After... |
| dot-commonSpecies | Get Matrix With UniProt Abbreviations For Selected Species As... |
| dot-extrSpecPref | Extract Additional Information To Construct The Colum... |
| dot-imputeNA | Basic NA-imputaton (main) |
| dot-plotQuantDistr | Generic Plotting Of Density Distribution For Quantitation... |
| exportAsWombatP | Export As Wombat-P Set Of Files |
| exportSdrfDraft | Export Sample Meta-data from Quantification-Software as... |
| extractTestingResults | Extract Results From Moderated t-tests |
| extrSpeciesAnnot | Extract species annotation |
| foldChangeArrow2 | Add arrow for expected Fold-Change to VolcanoPlot or MA-plot |
| fuseProteomicsProjects | Combine Multiple Proteomics Data-Sets |
| getUPS1acc | Accession-Numbers And Names Of UPS1 Proteins |
| inspectSpeciesIndic | Inspect Species Indictaion Or Group of Proteins |
| isolNAneighb | Isolate NA-neighbours |
| massDeFormula | Molecular mass from chemical formula |
| matrixNAinspect | Histogram of content of NAs in matrix |
| matrixNAneighbourImpute | Imputation of NA-values based on non-NA replicates |
| plotROC | Plot ROC curves |
| razorNoFilter | Filter based on either number of total peptides and specific... |
| readAlphaPeptFile | Read (Normalized) Quantitation Data Files Produced By... |
| readDiaNNFile | Read Tabulated Files Exported by DIA-NN At Protein Level |
| readDiaNNPeptides | Read Tabulated Files Exported by DiaNN At Peptide Level |
| readFasta2 | Read File Of Protein Sequences In Fasta Format |
| readFragpipeFile | Read Tabulated Files Exported by FragPipe At Protein Level |
| readIonbotPeptides | Read Tabulated Files Exported by Ionbot At Peptide Level |
| readMassChroQFile | Read tabulated files imported from MassChroQ |
| readMaxQuantFile | Read Quantitation Data-Files (proteinGroups.txt) Produced... |
| readMaxQuantPeptides | Read Peptide Identification and Quantitation Data-Files... |
| readOpenMSFile | Read csv files exported by OpenMS |
| readProlineFile | Read xlsx, csv or tsv files exported from Proline and... |
| readProtDiscovererPeptides | readProtDiscovererPeptides, depreciated |
| readProtDiscovFile | Read Tabulated Files Exported By ProteomeDiscoverer At... |
| readProtDiscovPeptides | Read Tabulated Files Exported by ProteomeDiscoverer At... |
| readProteomeDiscovererFile | Read Tabulated Files Exported By ProteomeDiscoverer At... |
| readProteomeDiscovererPeptides | Read Tabulated Files Exported by ProteomeDiscoverer At... |
| readSampleMetaData | Read Sample Meta-data from Quantification-Software And/Or... |
| readSdrf | Read proteomics meta-data as sdrf file |
| readUCSCtable | Read annotation files from UCSC |
| readUniProtExport | Read protein annotation as exported from UniProt... |
| readWombatNormFile | Read (Normalized) Quantitation Data Files Produced By Wombat... |
| removeSampleInList | Remove Samples/Columns From list of matrixes |
| replMissingProtNames | Complement Missing EntryNames In Annotation |
| shortSoftwName | Get Short Names of Proteomics Quantitation Software |
| summarizeForROC | Summarize statistical test result for plotting ROC-curves |
| test2grp | t-test each line of 2 groups of data |
| testRobustToNAimputation | Pair-wise testing robust to NA-imputation |
| VolcanoPlotW2 | Deprecialed Volcano-plot |
| writeFasta2 | Write sequences in fasta format to file This function writes... |
