Downstream analysis of the MaxQuant output


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Documentation for package ‘proteus’ version 0.2.16

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aggregateHifly Protein aggregate function using hifly method
aggregateMedian Protein/peptide aggregate function using median
aggregateSum Peptide/protein aggregate function using sum
allowedUniProtColumns Allowed UniProt columns
allProteinTable All protein table
annotateProteins Annotate proteins
evidenceColumns Evidence columns
fetchFromUniProt Fetch annotations from UniProt
goodData Create a table indicating good data.
intensityStats Statistics for an intensity table
jaccardSimilarity Jaccard similarity
jitterPlot Jitter plot
limmaDE Simple differential expression with limma
limmaRatioDE Simple one-sample differential expression with limma
makePeptideTable Create peptide table from evidence data
makeProteinTable Make protein table
measureColumns Measure columns
normalizeData Normalize proteus data
normalizeMedian Normalize columns of a matrix to medians
normalizeTMT Normalize protein/peptide data using CONSTANd normalization
parameterString Helper function, not exported
plotClustering Plot clustering dendrogram
plotCount Plot peptide or protein count per sample
plotDetectionSimilarity Detection Jaccard similarity
plotDistanceMatrix Plot distance matrix
plotFID Fold-change intensity diagram
plotFID_live Fold-change intensity diagram in live Shiny session
plotIntensities Plot protein/peptide intensities
plotMV Plot mean-variance relationship
plotPCA Plot PCA
plotPdist Plot p-value distribution
plotProtPeptides Protein-peptide plot
plotSampleDistributions Plot distribution of intensities/ratios for each sample
plotVolcano Volcano plot
plotVolcano_live Volcano plot in live Shiny session
proteinColumns Protein columns
proteinInfo Protein information
proteusData 'proteusData' constructor
RAS RAS procedure for CONSTANd normalization (not exported)
readColumnNames Read column names from a tab-delimited text file
readEvidenceFile Read MaxQuant's evidence file
readProteinGroups Read protein groups file from MaxQuant
replicateTable Replicate table
significanceTable Significance table
summary.proteusData Summary of 'proteusData' object
tryQuery Internal function to query UniProt