| .atomicMasses | Molecular mass for Elements |
| .checkKnitrProt | Checking presence of knitr and rmarkdown |
| .checkSetupGroups | Additional/final chek and adjustments to sample-order after readSampleMetaData() |
| .commonSpecies | Get matrix with UniProt abbreviations for selected species as well as simple names |
| .extrSpecPref | Extract additional information to construct colum SpecType |
| .imputeNA | Basic NA-imputaton (main) |
| .plotQuantDistr | Generic plotting of density distribution for quantitation import-functions |
| AAmass | Molecular mass for amino-acids |
| AucROC | AUC from ROC-curves |
| cleanListCoNames | Selective batch cleaning of sample- (ie column-) names in list |
| combineMultFilterNAimput | Combine Multiple Filters On NA-imputed Data |
| convAASeq2mass | Molecular mass for amino-acids |
| corColumnOrder | Order Columns in list of matrixes |
| countNoOfCommonPeptides | Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides. The in-silico digestion may be performed separately using the package cleaver. Note: input must be list (or multiple names lists) of proteins with their respective peptides (eg by in-silico digestion). |
| exportSdrfDraft | Export Sample Meta-data from Quantification-Software as Sdrf-draft |
| 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 UPS-1 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 peptides or number of razor petides |
| readAlphaPeptFile | Read (Normalized) Quantitation Data Files Produced By AlphaPept |
| 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 |
| readMassChroQFile | Read tabulated files imported from MassChroQ |
| readMaxQuantFile | Read Quantitation Data-Files (proteinGroups.txt) Produced From MaxQuant At Protein Level |
| readMaxQuantPeptides | Read Peptide Identificationa and Quantitation Data-Files (peptidess.txt) Produced By MaxQuant |
| readOpenMSFile | Read csv files exported by OpenMS |
| readProlineFile | Read xlsx, csv or tsv files exported from Proline and MS-Angel |
| readProtDiscovererPeptides | readProtDiscovererPeptides, depreciated |
| readProtDiscovFile | Read Tabulated Files Exported By ProteomeDiscoverer At Protein Level, Deprecated |
| readProtDiscovPeptides | Read Tabulated Files Exported by ProteomeDiscoverer At Peptide Level, Deprecated |
| readProteomeDiscovererFile | Read Tabulated Files Exported By ProteomeDiscoverer At Protein Level |
| readProteomeDiscovererPeptides | Read Tabulated Files Exported by ProteomeDiscoverer At Peptide Level |
| readSampleMetaData | Read Sample Meta-data from Quantification-Software And/Or Sdrf And Align To Experimental Data |
| readSdrf | Read proteomics meta-data as sdrf file |
| readUCSCtable | Read annotation files from UCSC |
| readUniProtExport | Read protein annotation as exported from UniProt batch-conversion |
| readWombatNormFile | Read (Normalized) Quantitation Data Files Produced By Wombat At Protein Level |
| 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 sequences from character vector as fasta formatted file (from UniProt) Line-headers are based on names of elements of input vector 'prot'. This function also allows comparing the main vector of sequences with a reference vector 'ref' to check if any of the sequences therein are truncated. |