IdMappingAnalysis: ID Mapping Analysis

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Identifier mapping performance analysis

Author
Alex Lisovich, Roger Day
Date of publication
None
Maintainer
Alex Lisovich <alex.lisovich@gmail.com>, Roger Day <day01@pitt.edu>
License
GPL-2
Version
1.18.0

View on Bioconductor

Man pages

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

Files in this package

IdMappingAnalysis/DESCRIPTION
IdMappingAnalysis/NAMESPACE
IdMappingAnalysis/R
IdMappingAnalysis/R/IdMappingAnalysis-package.R
IdMappingAnalysis/R/bootstrap.R
IdMappingAnalysis/R/corr.R
IdMappingAnalysis/R/corrData.R
IdMappingAnalysis/R/data.R
IdMappingAnalysis/R/dataFilter.R
IdMappingAnalysis/R/display.R
IdMappingAnalysis/R/expectedUtility.R
IdMappingAnalysis/R/fit2clusters.R
IdMappingAnalysis/R/idMap.R
IdMappingAnalysis/R/idMapBase.R
IdMappingAnalysis/R/idMapCounts.R
IdMappingAnalysis/R/idMapDiff.R
IdMappingAnalysis/R/idMapDiffCounts.R
IdMappingAnalysis/R/jointIdMap.R
IdMappingAnalysis/R/jointIdMap.plots.R
IdMappingAnalysis/R/jointUniquePairs.R
IdMappingAnalysis/R/jointUniquePairs.extensions.R
IdMappingAnalysis/R/jointUniquePairs.interactive.plots.R
IdMappingAnalysis/R/jointUniquePairs.plots.R
IdMappingAnalysis/R/misc.R
IdMappingAnalysis/R/mixture.R
IdMappingAnalysis/R/subset.R
IdMappingAnalysis/R/uniquePairs.R
IdMappingAnalysis/R/zzz.R
IdMappingAnalysis/build
IdMappingAnalysis/build/vignette.rds
IdMappingAnalysis/data
IdMappingAnalysis/data/datalist
IdMappingAnalysis/data/examples.RData
IdMappingAnalysis/demo
IdMappingAnalysis/demo/00Index
IdMappingAnalysis/demo/DataAnalysis.R
IdMappingAnalysis/demo/InteractiveDataAnalysis.R
IdMappingAnalysis/demo/readECMdoc.R
IdMappingAnalysis/inst
IdMappingAnalysis/inst/doc
IdMappingAnalysis/inst/doc/IdMappingAnalysis.R
IdMappingAnalysis/inst/doc/IdMappingAnalysis.Rnw
IdMappingAnalysis/inst/doc/IdMappingAnalysis.pdf
IdMappingAnalysis/man
IdMappingAnalysis/man/000-LB-.IdMapBase.Rd
IdMappingAnalysis/man/Bootstrap.Rd
IdMappingAnalysis/man/Corr.Rd
IdMappingAnalysis/man/CorrData.Rd
IdMappingAnalysis/man/CsvList.merge.Misc.Rd
IdMappingAnalysis/man/DataFilter.Rd
IdMappingAnalysis/man/Display.Rd
IdMappingAnalysis/man/Generic.Roo.Rd
IdMappingAnalysis/man/IdMap.Rd
IdMappingAnalysis/man/IdMapBase.Rd
IdMappingAnalysis/man/IdMapCounts.Rd
IdMappingAnalysis/man/IdMapDiff.Rd
IdMappingAnalysis/man/IdMapDiffCounts.Rd
IdMappingAnalysis/man/JointIdMap.Rd
IdMappingAnalysis/man/JointUniquePairs.Rd
IdMappingAnalysis/man/Misc.Rd
IdMappingAnalysis/man/Mixture.Rd
IdMappingAnalysis/man/Subset.Rd
IdMappingAnalysis/man/UniquePairs.Rd
IdMappingAnalysis/man/aligned.IdMapBase.Rd
IdMappingAnalysis/man/as.IdMap.UniquePairs.Rd
IdMappingAnalysis/man/as.MultiSet.CorrData.Rd
IdMappingAnalysis/man/as.UniquePairs.IdMap.Rd
IdMappingAnalysis/man/as.data.frame.IdMapBase.Rd
IdMappingAnalysis/man/as.data.frame.JointIdMap.Rd
IdMappingAnalysis/man/as.list.IdMap.Rd
IdMappingAnalysis/man/boxplot.JointUniquePairs.Rd
IdMappingAnalysis/man/boxplotdataJitter.JointUniquePairs.Rd
IdMappingAnalysis/man/byColNames.Subset.Rd
IdMappingAnalysis/man/byColumn.Subset.Rd
IdMappingAnalysis/man/byRow.Subset.Rd
IdMappingAnalysis/man/byRowNames.Subset.Rd
IdMappingAnalysis/man/clust.Mixture.Rd
IdMappingAnalysis/man/copy.Display.Rd
IdMappingAnalysis/man/corr.boxplot.JointUniquePairs.Rd
IdMappingAnalysis/man/corr.plot.JointUniquePairs.Rd
IdMappingAnalysis/man/create.Display.Rd
IdMappingAnalysis/man/create.UniquePairs.Rd
IdMappingAnalysis/man/diffCounts.plot.JointIdMap.Rd
IdMappingAnalysis/man/dim.IdMapBase.Rd
IdMappingAnalysis/man/dimnames.IdMapBase.Rd
IdMappingAnalysis/man/do.apply.DataFilter.Rd
IdMappingAnalysis/man/do.glm.JointUniquePairs.Rd
IdMappingAnalysis/man/ecdf.plot.JointIdMap.Rd
IdMappingAnalysis/man/equals.UniquePairs.Rd
IdMappingAnalysis/man/examples.Rd
IdMappingAnalysis/man/expectedUtility.Rd
IdMappingAnalysis/man/fisherTransform.DataFilter.Rd
IdMappingAnalysis/man/fisherTransformInverse.DataFilter.Rd
IdMappingAnalysis/man/fisherTransformJacobean.DataFilter.Rd
IdMappingAnalysis/man/fit2clusters.Rd
IdMappingAnalysis/man/getBootstrap.JointUniquePairs.Rd
IdMappingAnalysis/man/getCompoundEvents.IdMapDiffCounts.Rd
IdMappingAnalysis/man/getCompoundGroups.IdMapDiffCounts.Rd
IdMappingAnalysis/man/getCorr.JointUniquePairs.Rd
IdMappingAnalysis/man/getCorrData.JointUniquePairs.Rd
IdMappingAnalysis/man/getCorrDataFrame.JointUniquePairs.Rd
IdMappingAnalysis/man/getCounts.IdMap.Rd
IdMappingAnalysis/man/getCounts.JointIdMap.Rd
IdMappingAnalysis/man/getData.Corr.Rd
IdMappingAnalysis/man/getData.Mixture.Rd
IdMappingAnalysis/man/getDiff.JointIdMap.Rd
IdMappingAnalysis/man/getExperimentSet.CorrData.Rd
IdMappingAnalysis/man/getIdMapList.JointIdMap.Rd
IdMappingAnalysis/man/getMapNames.JointIdMap.Rd
IdMappingAnalysis/man/getMapNames.JointUniquePairs.Rd
IdMappingAnalysis/man/getMatch.UniquePairs.Rd
IdMappingAnalysis/man/getMatchInfo.JointIdMap.Rd
IdMappingAnalysis/man/getMatchInfo.JointUniquePairs.Rd
IdMappingAnalysis/man/getMixture.JointUniquePairs.Rd
IdMappingAnalysis/man/getName.IdMapBase.Rd
IdMappingAnalysis/man/getSampleNames.CorrData.Rd
IdMappingAnalysis/man/getStats.IdMapCounts.Rd
IdMappingAnalysis/man/getStats.Mixture.Rd
IdMappingAnalysis/man/getUnionIdMap.JointIdMap.Rd
IdMappingAnalysis/man/getUniquePairs.Corr.Rd
IdMappingAnalysis/man/getUniquePairs.CorrData.Rd
IdMappingAnalysis/man/getUniquePairs.JointUniquePairs.Rd
IdMappingAnalysis/man/interactive.corr.boxplot.JointUniquePairs.Rd
IdMappingAnalysis/man/interactive.corr.plot.JointUniquePairs.Rd
IdMappingAnalysis/man/interactive.mixture.boxplot.JointUniquePairs.Rd
IdMappingAnalysis/man/interactive.mixture.plot.JointUniquePairs.Rd
IdMappingAnalysis/man/interactive.plot.CorrData.Rd
IdMappingAnalysis/man/interactive.plot.JointUniquePairs.Rd
IdMappingAnalysis/man/interleave.Misc.Rd
IdMappingAnalysis/man/line.loess.Display.Rd
IdMappingAnalysis/man/line.unsorted.Display.Rd
IdMappingAnalysis/man/logTen.DataFilter.Rd
IdMappingAnalysis/man/merge.IdMap.Rd
IdMappingAnalysis/man/minAvgCountConstraint.DataFilter.Rd
IdMappingAnalysis/man/minCountConstraint.DataFilter.Rd
IdMappingAnalysis/man/minCountGroupConstraint.DataFilter.Rd
IdMappingAnalysis/man/mixture.boxplot.JointUniquePairs.Rd
IdMappingAnalysis/man/mixture.plot.JointUniquePairs.Rd
IdMappingAnalysis/man/pack.experiments.CorrData.Rd
IdMappingAnalysis/man/plot.Bootstrap.Rd
IdMappingAnalysis/man/plot.Corr.Rd
IdMappingAnalysis/man/plot.CorrData.Rd
IdMappingAnalysis/man/plot.IdMapCounts.Rd
IdMappingAnalysis/man/plot.IdMapDiffCounts.Rd
IdMappingAnalysis/man/plot.Mixture.Rd
IdMappingAnalysis/man/primaryIDs.IdMapBase.Rd
IdMappingAnalysis/man/primaryKey.CorrData.Rd
IdMappingAnalysis/man/primaryKey.IdMapBase.Rd
IdMappingAnalysis/man/primaryKey.Mixture.Rd
IdMappingAnalysis/man/progressMsg.Display.Rd
IdMappingAnalysis/man/removeNASeries.DataFilter.Rd
IdMappingAnalysis/man/secondaryKey.CorrData.Rd
IdMappingAnalysis/man/secondaryKey.IdMapBase.Rd
IdMappingAnalysis/man/secondaryKey.Mixture.Rd
IdMappingAnalysis/man/subsetCorr.JointUniquePairs.Rd
IdMappingAnalysis/man/subsetData.JointUniquePairs.Rd
IdMappingAnalysis/man/subsetGroups.JointUniquePairs.Rd
IdMappingAnalysis/man/summary.IdMapDiffCounts.Rd
IdMappingAnalysis/man/swapKeys.IdMap.Rd
IdMappingAnalysis/man/swapKeys.UniquePairs.Rd
IdMappingAnalysis/man/textBoundingBox.Display.Rd
IdMappingAnalysis/man/to.base.Misc.Rd
IdMappingAnalysis/man/to.binary.logical.Misc.Rd
IdMappingAnalysis/man/to.index.expr.Misc.Rd
IdMappingAnalysis/man/unique.UniquePairs.Rd
IdMappingAnalysis/man/words.Misc.Rd
IdMappingAnalysis/man/zoom.pars.Display.Rd
IdMappingAnalysis/vignettes
IdMappingAnalysis/vignettes/ECM_algorithm_for_two_clusters.pdf
IdMappingAnalysis/vignettes/IdMappingAnalysis.Rnw