Man pages for IdMappingAnalysis
ID Mapping Analysis
| 000-LB-.IdMapBase | Access the elements of a data frame encapsulated within the... |
| aligned.IdMapBase | Checks if two IdMapBase objects match on column names and... |
| as.data.frame.IdMapBase | Retrieves a data frame encapsulated within the given... |
| as.data.frame.JointIdMap | Retrieve a data frame encapsulated within the given... |
| as.IdMap.UniquePairs | Convert the UniquePairs object into the IdMap object |
| as.list.IdMap | Coerce an object or a list of compatible object to the IdMap... |
| as.MultiSet.CorrData | Convert CorrData object into MultiSet object |
| as.UniquePairs.IdMap | Create a UniquePairs object from a given IdMap object |
| Bootstrap | The Bootstrap class |
| boxplotdataJitter.JointUniquePairs | Plot a set of points representing the density distribution of... |
| boxplot.JointUniquePairs | Draw a basic boxplot based on a given JointUniquePairs object... |
| byColNames.Subset | Extract subset of columns from a data frame or a list of data... |
| byColumn.Subset | # Extract subset of rows from a data frame or a list of data... |
| byRowNames.Subset | Extract subset of columns from a data frame or a list of data... |
| byRow.Subset | Extract subset of columns from a data frame or a list of data... |
| clust.Mixture | Retrieve the custering results data structure |
| copy.Display | Save current plot to the file |
| Corr | The Corr class |
| corr.boxplot.JointUniquePairs | Boxplot of correlations by match group |
| CorrData | CorrData class |
| corr.plot.JointUniquePairs | Plot the density distributions for a set of correlation... |
| create.Display | Open a new display device |
| create.UniquePairs | Create a UniquePairs object from a single IdMap or a list of... |
| CsvList.merge.Misc | Pairwise merge of two string vectors |
| DataFilter | The DataFilter class |
| diffCounts.plot.JointIdMap | Interactive wrapper for IdMapDiffCounts$plot |
| dim.IdMapBase | Retrieves dimensions of data frame encapsulated within the... |
| dimnames.IdMapBase | Retrieve or set the dimnames of data frame encapsulated... |
| Display | The Display class |
| do.apply.DataFilter | Filter experiment using constraints |
| do.glm.JointUniquePairs | Compute linear regression for the given set of ID Maps |
| ecdf.plot.JointIdMap | Interactive wrapper for IdMapCounts$plot |
| equals.UniquePairs | Check if two unique pairs data structures are identical |
| examples | IdMappingAnalysis sample data... |
| expectedUtility | Expected utility of an ID mapping, ID filtering, or other... |
| fisherTransform.DataFilter | Compute the Fisher transform |
| fisherTransformInverse.DataFilter | Compute the Fisher inversed transform |
| fisherTransformJacobean.DataFilter | Compute the Fisher transform Jacobean |
| fit2clusters | Flexible two-cluster mixture fit of a numeric vector |
| Generic.Roo | Generic R.00 objects |
| getBootstrap.JointUniquePairs | Create Bootstrap object from JointUniquePairs object and two... |
| getCompoundEvents.IdMapDiffCounts | Get compound events |
| getCompoundGroups.IdMapDiffCounts | Get counts for each compound event in IdMapDiffCounts |
| getCorrDataFrame.JointUniquePairs | Merge JointUniquePairs and Corr objects into a single data... |
| getCorrData.JointUniquePairs | Create CorrData object from the JointUniquePairs object and... |
| getCorr.JointUniquePairs | Extract a set of correlation objects from given... |
| getCounts.IdMap | Compute the count of secondaryIDs for each primary ID |
| getCounts.JointIdMap | Create an IdMapCounts object |
| getData.Corr | Extract correlation results from the Corr object |
| getData.Mixture | Extract mixture component data from the Mixture object |
| getDiff.JointIdMap | Create an IdMapDiff object |
| getExperimentSet.CorrData | Get experiment set data frame for a given modality |
| getIdMapList.JointIdMap | Create an Id Map list from a JointIdMap object |
| getMapNames.JointIdMap | Get the names of IdMap objects encapsulated within the given... |
| getMapNames.JointUniquePairs | Get the names of UniquePairs objects encapsulated within the... |
| getMatchInfo.JointIdMap | Get match table(s) for a given set of primary IDs |
| getMatchInfo.JointUniquePairs | Get match table(s) for a given set of primary IDs |
| getMatch.UniquePairs | Get the logical vector of pair matches of the given... |
| getMixture.JointUniquePairs | Extract mixture model object from JointUniquePairs and Corr... |
| getName.IdMapBase | Get the name a given IdMapBase object |
| getSampleNames.CorrData | Get experiment sample names |
| getStats.IdMapCounts | Retrieves a set of unique counts of secondary IDs |
| getStats.Mixture | Get mixture component model summary info |
| getUnionIdMap.JointIdMap | Create a union IdMap |
| getUniquePairs.Corr | Extract unique pairs from the Corr object |
| getUniquePairs.CorrData | Extract unique pairs from the CorrData object |
| getUniquePairs.JointUniquePairs | Extract the unity UniquePairs object from a given... |
| IdMap | The ID Map class |
| IdMapBase | The ID Map base class |
| IdMapCounts | The IdMapCounts class |
| IdMapDiff | The IdMapDiff class |
| IdMapDiffCounts | The IdMapDiffCounts class |
| interactive.corr.boxplot.JointUniquePairs | Interactive boxplot of correlations by match group |
| interactive.corr.plot.JointUniquePairs | Interactive plot of correlation densities |
| interactive.mixture.boxplot.JointUniquePairs | Interactive boxplot of mixture component probabilities by... |
| interactive.mixture.plot.JointUniquePairs | Interactive plot of mixture model components |
| interactive.plot.CorrData | Draw a scatterplot of experiment data interactively |
| interactive.plot.JointUniquePairs | General purpose JointUniquePairs interactive plot function |
| interleave.Misc | Interleave two matrixes by columns |
| JointIdMap | The Joint ID Map class |
| JointUniquePairs | The JointUniquePairs class |
| line.loess.Display | Plot loess transformed data |
| line.unsorted.Display | Draw a curve from unsorted points |
| logTen.DataFilter | Compute log10 of a numerical vector combined with... |
| merge.IdMap | Merge the IdMap object with a second IdMap object or a list... |
| minAvgCountConstraint.DataFilter | Perform mean based thresholding of an input vector |
| minCountConstraint.DataFilter | Perform minimum count based thresholding of an input vector |
| minCountGroupConstraint.DataFilter | Perform minimum count based thresholding of an input vector... |
| Misc | The Misc class |
| Mixture | The Mixture class |
| mixture.boxplot.JointUniquePairs | Boxplot of a mixture model component by match group |
| mixture.plot.JointUniquePairs | Plot the correlation densities of the empirical fit, mixture... |
| pack.experiments.CorrData | Convert aligned experiment data into the data structure... |
| plot.Bootstrap | Scatterplot of bootstrapped results: sd vs correlation |
| plot.Corr | Plot the density distributions for correlation object(s) |
| plot.CorrData | Scatterplot of experiment data |
| plot.IdMapCounts | Compute and plot the (inversed) ecdf for each ID Map count... |
| plot.IdMapDiffCounts | Produce a fountain plot representing the quantitative... |
| plot.Mixture | Plot the results of mixture modeling |
| primaryIDs.IdMapBase | Retrieves the primary IDs for a given IdMapBase object |
| primaryKey.CorrData | Retrieves a primary key for a given CorrData object |
| primaryKey.IdMapBase | Retrieves a primary key for a given IdMapBase object |
| primaryKey.Mixture | Retrieves a primary key for a given Mixture object |
| progressMsg.Display | Display a progress message |
| removeNASeries.DataFilter | Remove NA series from the experiment set |
| secondaryKey.CorrData | Retrieves a secondary key for a given CorrData object |
| secondaryKey.IdMapBase | Retrieves a secondary key for a given IdMapBase object |
| secondaryKey.Mixture | Retrieves a secondary key for a given Mixture object |
| Subset | The Subset class |
| subsetCorr.JointUniquePairs | Subset the Corr object |
| subsetData.JointUniquePairs | Subset data on a UniquePairsMatch object |
| subsetGroups.JointUniquePairs | Get a JointUniquePairs subset |
| summary.IdMapDiffCounts | Get a compaund event counts summary report |
| swapKeys.IdMap | Swap the primary and secondary key columns |
| swapKeys.UniquePairs | Swap the primary and secondary key columns |
| textBoundingBox.Display | Determine the size of the text bounding box |
| to.base.Misc | Convert number to a numeric vector of a given base |
| to.binary.logical.Misc | Convert number to a vector of logicals |
| to.index.expr.Misc | Convert expression into index expression for a given list or... |
| UniquePairs | The UniquePairs class |
| unique.UniquePairs | Extract unique elements |
| words.Misc | Convert space delimited string to a vector of words |
| zoom.pars.Display | Zoom graphics parameters |
