# Proteomics Data Analysis Functions

## Documentation for package ‘wrProteo’ version 2.0.2

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

## Help Pages

.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
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
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 | 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
readProtDiscovererPeptides | readProtDiscovererPeptides, deprecated
readProtDiscovFile | Read Tabulated Files Exported By ProteomeDiscoverer At Protein 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 | Pairwise Testing Robust To NA-Imputation
VolcanoPlotW2 | Deprecialed Volcano-plot
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.