Proteomics Data Analysis Functions


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Documentation for package ‘wrProteo’ version 1.6.0

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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.