# Proteomics Data Analysis Functions

## Documentation for package ‘wrProteo’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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 (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).
extractTestingResults | Extract results from moderated t-tests
extrSpeciesAnnot | Extract species annotation
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
VolcanoPlotW2 | Volcano-plot (Statistical Test Outcome versus Relative Change)
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.