Man pages for Vitek-Lab/MSstatsTMT
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
| annotation.mine | Example of annotation file for raw.mine, which is the output... |
| annotation.mq | Example of annotation file for evidence, which is the output... |
| annotation.pd | Example of annotation file for raw.pd, which is the PSM... |
| dataProcessPlotsTMT | Visualization for explanatory data analysis - TMT experiment |
| dot-checkContrastMatrix | check whether pairwise comparison. If pairwise, generate a... |
| dot-checkSummarizationParams | Check validity of parameters to proteinSummarization function |
| dot-countRunsWithNorm | Utility function: count runs with "Norm" channel |
| dot-documentFunction | A dummy function to store shared documentation items. |
| dot-getNormalizationAbundance | Utility function: get mean abundance for "Norm" channels |
| dot-getPhilosopherInput | Convert Philosopher parameters to consistent format |
| dot-getRunsMedian | Utility function: get median from unique values per run |
| dot-handleSingleContrastTMT | perform statistical inference for single protein and single... |
| dot-logSum | Utility function: compute log of sum of 2^x |
| dot-logSummarizationParams | Log parameters for proteinSummarization function |
| dot-makeContrastSingleTMT | Make a contrast |
| dot-makeFactorColumnsTMT | Converts required columns to factor in summarization output |
| dot-medianPolish | Tukey median polish |
| dot-normalizePeptides | Normalization between channels (before summarization) |
| dot-normalizeProteins | Normalization between MS runs (after protein summarization) |
| dot-prepareForSummarization | Prepare TMT data for protein-level summarization |
| dot-removeRedundantChannels | Remove empty and normalization channels |
| dot-summarizeMSstats | Summarization based on MSstats |
| dot-summarizeSimpleStat | Summarize TMT data with a simple aggregate of log-intensities |
| dot-summarizeTMP | Summarize TMT data with median polish |
| dot-summarizeTMT | Performs summarization for TMT data |
| evidence | Example of output from MaxQuant for TMT-10plex experiments. |
| getProcessedTMT | Get processed feature-level data |
| getSummarizedTMT | Get protein-level data from MSstatsSummarizeTMT output |
| groupComparisonTMT | Finding differentially abundant proteins across conditions in... |
| input.pd | Example of output from PDtoMSstatsTMTFormat function |
| MaxQtoMSstatsTMTFormat | Generate MSstatsTMT required input format from MaxQuant... |
| MSstatsComparisonModelSingleTMT | Fit a linear model for group comparison for a single protein |
| MSstatsFitComparisonModelsTMT | Fit linear models for group comparison |
| MSstatsGroupComparisonOutputTMT | Combine testing results for individual proteins |
| MSstatsGroupComparisonTMT | Group comparison for TMT data |
| MSstatsModerateTTest | Moderate T statistic for group comparison |
| MSstatsNormalizeTMT | Normalization for TMT data |
| MSstatsPrepareForGroupComparisonTMT | Prepare output of proteinSummarization for group comparison |
| MSstatsPrepareForSummarizationTMT | Prepare output of MSstatsTMT converters for protein-level... |
| MSstatsSummarizationOutputTMT | Combine feature-level and protein-level data into single... |
| MSstatsSummarizeTMT | Protein summarization for TMT data |
| MSstatsTestSingleProteinTMT | Hypothesis tests for a single protein in TMT data |
| MSstatsTMT | MSstatsTMT: A package for protein significance analysis in... |
| OpenMStoMSstatsTMTFormat | Generate MSstatsTMT required input format for OpenMS output |
| PDtoMSstatsTMTFormat | Convert Proteome Discoverer output to MSstatsTMT format. |
| PhilosophertoMSstatsTMTFormat | Convert Philosopher (Fragpipe) output to MSstatsTMT format. |
| proteinGroups | Example of proteinGroups file from MaxQuant for TMT-10plex... |
| proteinSummarization | Summarizing peptide level quantification to protein level... |
| quant.pd.msstats | Example of output from proteinSummarizaiton function |
| raw.mine | Example of output from SpectroMine for TMT-6plex experiments. |
| raw.om | Example of MSstatsTMT report from OpenMS for TMT-10plex... |
| raw.pd | Example of output from Proteome Discoverer 2.2 for TMT-10plex... |
| SpectroMinetoMSstatsTMTFormat | Import data from SpectroMine |
| test.pairwise | Example of output from groupComparisonTMT function |
