Proteomics Data Analysis Functions

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Documentation for package ‘wrProteo’ version 1.12.0

• 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 chek 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 colum SpecType
.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 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).
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	Accession-Numbers And Names Of UPS1 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.