Man pages for IdMappingAnalysis
ID Mapping Analysis

000-LB-.IdMapBaseAccess the elements of a data frame encapsulated within the...
aligned.IdMapBaseChecks if two IdMapBase objects match on column names and...
as.data.frame.IdMapBaseRetrieves a data frame encapsulated within the given...
as.data.frame.JointIdMapRetrieve a data frame encapsulated within the given...
as.IdMap.UniquePairsConvert the UniquePairs object into the IdMap object
as.list.IdMapCoerce an object or a list of compatible object to the IdMap...
as.MultiSet.CorrDataConvert CorrData object into MultiSet object
as.UniquePairs.IdMapCreate a UniquePairs object from a given IdMap object
BootstrapThe Bootstrap class
boxplotdataJitter.JointUniquePairsPlot a set of points representing the density distribution of...
boxplot.JointUniquePairsDraw a basic boxplot based on a given JointUniquePairs object...
byColNames.SubsetExtract 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.SubsetExtract subset of columns from a data frame or a list of data...
byRow.SubsetExtract subset of columns from a data frame or a list of data...
clust.MixtureRetrieve the custering results data structure
copy.DisplaySave current plot to the file
CorrThe Corr class
corr.boxplot.JointUniquePairsBoxplot of correlations by match group
CorrDataCorrData class
corr.plot.JointUniquePairsPlot the density distributions for a set of correlation...
create.DisplayOpen a new display device
create.UniquePairsCreate a UniquePairs object from a single IdMap or a list of...
CsvList.merge.MiscPairwise merge of two string vectors
DataFilterThe DataFilter class
diffCounts.plot.JointIdMapInteractive wrapper for IdMapDiffCounts$plot
dim.IdMapBaseRetrieves dimensions of data frame encapsulated within the...
dimnames.IdMapBaseRetrieve or set the dimnames of data frame encapsulated...
DisplayThe Display class
do.apply.DataFilterFilter experiment using constraints
do.glm.JointUniquePairsCompute linear regression for the given set of ID Maps
ecdf.plot.JointIdMapInteractive wrapper for IdMapCounts$plot
equals.UniquePairsCheck if two unique pairs data structures are identical
examplesIdMappingAnalysis sample data...
expectedUtilityExpected utility of an ID mapping, ID filtering, or other...
fisherTransform.DataFilterCompute the Fisher transform
fisherTransformInverse.DataFilterCompute the Fisher inversed transform
fisherTransformJacobean.DataFilterCompute the Fisher transform Jacobean
fit2clustersFlexible two-cluster mixture fit of a numeric vector
Generic.RooGeneric R.00 objects
getBootstrap.JointUniquePairsCreate Bootstrap object from JointUniquePairs object and two...
getCompoundEvents.IdMapDiffCountsGet compound events
getCompoundGroups.IdMapDiffCountsGet counts for each compound event in IdMapDiffCounts
getCorrDataFrame.JointUniquePairsMerge JointUniquePairs and Corr objects into a single data...
getCorrData.JointUniquePairsCreate CorrData object from the JointUniquePairs object and...
getCorr.JointUniquePairsExtract a set of correlation objects from given...
getCounts.IdMapCompute the count of secondaryIDs for each primary ID
getCounts.JointIdMapCreate an IdMapCounts object
getData.CorrExtract correlation results from the Corr object
getData.MixtureExtract mixture component data from the Mixture object
getDiff.JointIdMapCreate an IdMapDiff object
getExperimentSet.CorrDataGet experiment set data frame for a given modality
getIdMapList.JointIdMapCreate an Id Map list from a JointIdMap object
getMapNames.JointIdMapGet the names of IdMap objects encapsulated within the given...
getMapNames.JointUniquePairsGet the names of UniquePairs objects encapsulated within the...
getMatchInfo.JointIdMapGet match table(s) for a given set of primary IDs
getMatchInfo.JointUniquePairsGet match table(s) for a given set of primary IDs
getMatch.UniquePairsGet the logical vector of pair matches of the given...
getMixture.JointUniquePairsExtract mixture model object from JointUniquePairs and Corr...
getName.IdMapBaseGet the name a given IdMapBase object
getSampleNames.CorrDataGet experiment sample names
getStats.IdMapCountsRetrieves a set of unique counts of secondary IDs
getStats.MixtureGet mixture component model summary info
getUnionIdMap.JointIdMapCreate a union IdMap
getUniquePairs.CorrExtract unique pairs from the Corr object
getUniquePairs.CorrDataExtract unique pairs from the CorrData object
getUniquePairs.JointUniquePairsExtract the unity UniquePairs object from a given...
IdMapThe ID Map class
IdMapBaseThe ID Map base class
IdMapCountsThe IdMapCounts class
IdMapDiffThe IdMapDiff class
IdMapDiffCountsThe IdMapDiffCounts class
interactive.corr.boxplot.JointUniquePairsInteractive boxplot of correlations by match group
interactive.corr.plot.JointUniquePairsInteractive plot of correlation densities
interactive.mixture.boxplot.JointUniquePairsInteractive boxplot of mixture component probabilities by...
interactive.mixture.plot.JointUniquePairsInteractive plot of mixture model components
interactive.plot.CorrDataDraw a scatterplot of experiment data interactively
interactive.plot.JointUniquePairsGeneral purpose JointUniquePairs interactive plot function
interleave.MiscInterleave two matrixes by columns
JointIdMapThe Joint ID Map class
JointUniquePairsThe JointUniquePairs class
line.loess.DisplayPlot loess transformed data
line.unsorted.DisplayDraw a curve from unsorted points
logTen.DataFilterCompute log10 of a numerical vector combined with...
merge.IdMapMerge the IdMap object with a second IdMap object or a list...
minAvgCountConstraint.DataFilterPerform mean based thresholding of an input vector
minCountConstraint.DataFilterPerform minimum count based thresholding of an input vector
minCountGroupConstraint.DataFilterPerform minimum count based thresholding of an input vector...
MiscThe Misc class
MixtureThe Mixture class
mixture.boxplot.JointUniquePairsBoxplot of a mixture model component by match group
mixture.plot.JointUniquePairsPlot the correlation densities of the empirical fit, mixture...
pack.experiments.CorrDataConvert aligned experiment data into the data structure...
plot.BootstrapScatterplot of bootstrapped results: sd vs correlation
plot.CorrPlot the density distributions for correlation object(s)
plot.CorrDataScatterplot of experiment data
plot.IdMapCountsCompute and plot the (inversed) ecdf for each ID Map count...
plot.IdMapDiffCountsProduce a fountain plot representing the quantitative...
plot.MixturePlot the results of mixture modeling
primaryIDs.IdMapBaseRetrieves the primary IDs for a given IdMapBase object
primaryKey.CorrDataRetrieves a primary key for a given CorrData object
primaryKey.IdMapBaseRetrieves a primary key for a given IdMapBase object
primaryKey.MixtureRetrieves a primary key for a given Mixture object
progressMsg.DisplayDisplay a progress message
removeNASeries.DataFilterRemove NA series from the experiment set
secondaryKey.CorrDataRetrieves a secondary key for a given CorrData object
secondaryKey.IdMapBaseRetrieves a secondary key for a given IdMapBase object
secondaryKey.MixtureRetrieves a secondary key for a given Mixture object
SubsetThe Subset class
subsetCorr.JointUniquePairsSubset the Corr object
subsetData.JointUniquePairsSubset data on a UniquePairsMatch object
subsetGroups.JointUniquePairsGet a JointUniquePairs subset
summary.IdMapDiffCountsGet a compaund event counts summary report
swapKeys.IdMapSwap the primary and secondary key columns
swapKeys.UniquePairsSwap the primary and secondary key columns
textBoundingBox.DisplayDetermine the size of the text bounding box
to.base.MiscConvert number to a numeric vector of a given base
to.binary.logical.MiscConvert number to a vector of logicals
to.index.expr.MiscConvert expression into index expression for a given list or...
UniquePairsThe UniquePairs class
unique.UniquePairsExtract unique elements
words.MiscConvert space delimited string to a vector of words
zoom.pars.DisplayZoom graphics parameters
IdMappingAnalysis documentation built on Nov. 1, 2018, 5:02 a.m.