# Proteomics Data Analysis Functions

## Documentation for package ‘wrProteo’ version 1.13.3

- 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)
.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, 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.