IdMappingAnalysis: ID Mapping Analysis

Identifier mapping performance analysis

AuthorAlex Lisovich, Roger Day
Date of publicationNone
MaintainerAlex Lisovich <alex.lisovich@gmail.com>, Roger Day <day01@pitt.edu>
LicenseGPL-2
Version1.18.0

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

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