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