AAmass                  Molecular mass for amino-acids
AucROC                  AUC from ROC-curves
VolcanoPlotW2           Volcano-plot (Statistical Test Outcome versus
                        Relative Change)
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 (or matrix)
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).
extrSpeciesAnnot        Extract species annotation
extractTestingResults   Extract results from moderated t-tests
foldChangeArrow2        Add arrow for expected Fold-Change to
                        VolcanoPlot or MA-plot
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
readFasta2              Read file of protein sequences in fasta format
                        Read fasta formatted file (from UniProt) to
                        extract (protein) sequences and name. If
                        'tableOut=TRUE' output may be organized as
                        matrix for separating meta-annotation (eg
                        uniqueIdentifier, entryName, proteinName, GN)
                        in separate columns.
readMassChroQFile       Read tabulated files imported from MassChroQ
readMaxQuantFile        Read proteinGroups.txt files exported from
                        MaxQuant
readOpenMSFile          Read csv files exported by OpenMS
readProlineFile         Read csv or txt files exported from Proline and
                        MS-Angel
readProtDiscovFile      Read tabulated files exported by
                        ProteomeDiscoverer
readSdrf                Read proteomics meta-data as sdrf file This
                        function allows reading proteomics meta-data
                        from sdrf file, as they are provided on
                        https://github.com/bigbio/proteomics-metadata-standard.
                        Then, a data.frame with all annotation data
                        will be returned. To stay conform with the
                        (non-obligatory) recommendations, column-names
                        will be shown as lower caps.  The package utils
                        must be installed.
readUCSCtable           Read annotation files from UCSC
readUniProtExport       Read protein annotation as exported from
                        UniProt batch-conversion
removeSampleInList      Remove samples/columns from list of matrixes
                        Remove samples (ie columns) from every instance
                        of list of matrixes. Note: This function
                        assumes same order of columns in list-elements
                        'listElem' !
replMissingProtNames    Complement missing EntryNames in annotation
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
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.
