Man pages for bartongroup/Proteus
Downstream analysis of the MaxQuant output

aggregateHiflyProtein aggregate function using hifly method
aggregateMedianProtein/peptide aggregate function using median
aggregateSumPeptide/protein aggregate function using sum
allowedUniProtColumnsAllowed UniProt columns
allProteinTableAll protein table
annotateProteinsAnnotate proteins
evidenceColumnsEvidence columns
fetchFromUniProtFetch annotations from UniProt
goodDataCreate a table indicating good data.
intensityStatsStatistics for an intensity table
jaccardSimilarityJaccard similarity
jitterPlotJitter plot
limmaDESimple differential expression with limma
limmaRatioDESimple one-sample differential expression with limma
makePeptideTableCreate peptide table from evidence data
makeProteinTableMake protein table
measureColumnsMeasure columns
normalizeDataNormalize proteus data
normalizeMedianNormalize columns of a matrix to medians
normalizeTMTNormalize protein/peptide data using CONSTANd normalization
parameterStringHelper function, not exported
plotClusteringPlot clustering dendrogram
plotCountPlot peptide or protein count per sample
plotDetectionSimilarityDetection Jaccard similarity
plotDistanceMatrixPlot distance matrix
plotFIDFold-change intensity diagram
plotFID_liveFold-change intensity diagram in live Shiny session
plotIntensitiesPlot protein/peptide intensities
plotMVPlot mean-variance relationship
plotPCAPlot PCA
plotPdistPlot p-value distribution
plotProtPeptidesProtein-peptide plot
plotSampleDistributionsPlot distribution of intensities/ratios for each sample
plotVolcanoVolcano plot
plotVolcano_liveVolcano plot in live Shiny session
proteinColumnsProtein columns
proteinInfoProtein information
proteusData'proteusData' constructor
RASRAS procedure for CONSTANd normalization (not exported)
readColumnNamesRead column names from a tab-delimited text file
readEvidenceFileRead MaxQuant's evidence file
readProteinGroupsRead protein groups file from MaxQuant
replicateTableReplicate table
significanceTableSignificance table
summary.proteusDataSummary of 'proteusData' object
tryQueryInternal function to query UniProt
bartongroup/Proteus documentation built on Sept. 12, 2022, 12:39 a.m.