.atomicMasses           Molecular mass for Elements
.checkKnitrProt         Checking presence of knitr and rmarkdown
.checkSetupGroups       Additional/final Check 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 The
                        Colum 'SpecType', Allows Adding Information
                        From Fasta
.imputeNA               Basic NA-imputaton (main)
.parseFastaHeader       Parse Fasta Header
.plotQuantDistr         Generic Plotting Of Density Distribution For
                        Quantitation Import-functions
AAmass                  Molecular mass for amino-acids
AucROC                  AUC from ROC-curves
VolcanoPlotW2           Deprecialed Volcano-plot
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, Data.frames
                        And Vectors
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).
exportAsWombatP         Export As Wombat-P Set Of Files
exportSdrfDraft         Export Sample Meta-data from
                        Quantification-Software as Sdrf-draft
extrSpeciesAnnot        Extract species annotation
extractTestingResults   Extract Results From Moderated t-tests
foldChangeArrow2        Add arrow for expected Fold-Change to
                        VolcanoPlot or MA-plot
fuseProteomicsProjects
                        Combine Multiple Proteomics Data-Sets
getUPS1acc              UniProt 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 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
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 From MaxQuant At
                        Protein Level
readMaxQuantPeptides    Read Peptide Identification and Quantitation
                        Data-Files (peptides.txt) Produced By MaxQuant
readOpenMSFile          Read csv files exported by OpenMS
readProlineFile         Read xlsx, csv or tsv Files Exported From
                        Proline And MS-Angel
readProtDiscovFile      Read Tabulated Files Exported By
                        ProteomeDiscoverer At Protein Level, Deprecated
readProtDiscovererPeptides
                        readProtDiscovererPeptides, 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
                        Pairwise Testing Robust To NA-Imputation
writeFasta2             Write Sequences In Fasta Format To File This
                        function writes sequences from character vector
                        or parsed matrix to file as fasta formatted
                        file (close to UniProt) 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.
