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IdMappingAnalysis (version 1.16.0)

ID Mapping Analysis

Description

Identifier mapping performance analysis

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Version

Version

1.16.0

License

GPL-2

Maintainer

Alex Lisovich

Last Published

February 15th, 2017

Functions in IdMappingAnalysis (1.16.0)

getCorr.JointUniquePairs

Extract a set of correlation objects from given JointUniquePairs object and corresponding Corr object
IdMapCounts

The IdMapCounts class
getMixture.JointUniquePairs

Extract mixture model object from JointUniquePairs and Corr objects
getData.Mixture

Extract mixture component data from the Mixture object
getSampleNames.CorrData

Get experiment sample names
Display$progressMsg

Display a progress message
subsetGroups.JointUniquePairs

Get a JointUniquePairs subset
IdMapDiffCounts

The IdMapDiffCounts class
Display

The Display class
CorrData

CorrData class
DataFilter$fisherTransform

Compute the Fisher transform
fit2clusters

Flexible two-cluster mixture fit of a numeric vector
IdMapDiff

The IdMapDiff class
IdMap$as.list

Coerce an object or a list of compatible object to the IdMap object or a list of IdMap objects
dim.IdMapBase

Retrieves dimensions of data frame encapsulated within the given IdMapBase object
getIdMapList.JointIdMap

Create an Id Map list from a JointIdMap object
getStats.Mixture

Get mixture component model summary info
getStats.IdMapCounts

Retrieves a set of unique counts of secondary IDs
interactive.plot.JointUniquePairs

General purpose JointUniquePairs interactive plot function
as.data.frame.JointIdMap

Retrieve a data frame encapsulated within the given JointIdMap object
plot.Bootstrap

Scatterplot of bootstrapped results: sd vs correlation
DataFilter$do.apply

Filter experiment using constraints
examples

IdMappingAnalysis sample data...
primaryKey.CorrData

Retrieves a primary key for a given CorrData object
boxplot.JointUniquePairs

Draw a basic boxplot based on a given JointUniquePairs object and external data
getMatchInfo.JointUniquePairs

Get match table(s) for a given set of primary IDs
getUniquePairs.CorrData

Extract unique pairs from the CorrData object
DataFilter$minCountConstraint

Perform minimum count based thresholding of an input vector
IdMapBase

The ID Map base class
primaryIDs.IdMapBase

Retrieves the primary IDs for a given IdMapBase object
Subset$byRow

Extract subset of columns from a data frame or a list of data frames by intersecting on a particular row
as.IdMap.UniquePairs

Convert the UniquePairs object into the IdMap object
IdMap

The ID Map class
getMatchInfo.JointIdMap

Get match table(s) for a given set of primary IDs
equals.UniquePairs

Check if two unique pairs data structures are identical
Display$line.loess

Plot loess transformed data
ecdf.plot.JointIdMap

Interactive wrapper for IdMapCounts$plot
corr.plot.JointUniquePairs

Plot the density distributions for a set of correlation objects derived from JointUniquePairs and Corr objects
primaryKey.IdMapBase

Retrieves a primary key for a given IdMapBase object
DataFilter$minAvgCountConstraint

Perform mean based thresholding of an input vector
getUniquePairs.Corr

Extract unique pairs from the Corr object
getCompoundGroups.IdMapDiffCounts

Get counts for each compound event in IdMapDiffCounts
as.UniquePairs.IdMap

Create a UniquePairs object from a given IdMap object
mixture.boxplot.JointUniquePairs

Boxplot of a mixture model component by match group
DataFilter$minCountGroupConstraint

Perform minimum count based thresholding of an input vector subdivided into groups
clust.Mixture

Retrieve the custering results data structure
diffCounts.plot.JointIdMap

Interactive wrapper for IdMapDiffCounts$plot
expectedUtility

Expected utility of an ID mapping, ID filtering, or other bioinformatics data preparation method
getCorrDataFrame.JointUniquePairs

Merge JointUniquePairs and Corr objects into a single data frame
do.glm.JointUniquePairs

Compute linear regression for the given set of ID Maps
getBootstrap.JointUniquePairs

Create Bootstrap object from JointUniquePairs object and two experiment sets
secondaryKey.CorrData

Retrieves a secondary key for a given CorrData object
getData.Corr

Extract correlation results from the Corr object
getName.IdMapBase

Get the name a given IdMapBase object
Display$line.unsorted

Draw a curve from unsorted points
getMatch.UniquePairs

Get the logical vector of pair matches of the given UniquePairs object in other UniquePair object(s)
getCorrData.JointUniquePairs

Create CorrData object from the JointUniquePairs object and two experiment sets
interactive.mixture.boxplot.JointUniquePairs

Interactive boxplot of mixture component probabilities by match group
Generic R.00 objects

Generic R.00 objects
mixture.plot.JointUniquePairs

Plot the correlation densities of the empirical fit, mixture fit and each of the mixture components for a mixture object derived from JointUniquePairsand Corr objects
getCounts.JointIdMap

Create an IdMapCounts object
DataFilter$logTen

Compute log10 of a numerical vector combined with thresholding on minimum value
UniquePairs$swapKeys

Swap the primary and secondary key columns
secondaryKey.Mixture

Retrieves a secondary key for a given Mixture object
Misc$to.base

Convert number to a numeric vector of a given base
merge.IdMap

Merge the IdMap object with a second IdMap object or a list of IdMap objects
unique.UniquePairs

Extract unique elements
DataFilter$removeNASeries

Remove NA series from the experiment set
summary.IdMapDiffCounts

Get a compaund event counts summary report
Misc$to.binary.logical

Convert number to a vector of logicals
plot.CorrData

Scatterplot of experiment data
IdMap$swapKeys

Swap the primary and secondary key columns
Bootstrap

The Bootstrap class
UniquePairs

The UniquePairs class
getMapNames.JointIdMap

Get the names of IdMap objects encapsulated within the given JointIdMap object
getUniquePairs.JointUniquePairs

Extract the unity UniquePairs object from a given JointUniquePairs object
Misc$words

Convert space delimited string to a vector of words
getUnionIdMap.JointIdMap

Create a union IdMap
Corr

The Corr class
Subset

The Subset class
interactive.plot.CorrData

Draw a scatterplot of experiment data interactively
dimnames.IdMapBase

Retrieve or set the dimnames of data frame encapsulated within the given IdMapBase object
getExperimentSet.CorrData

Get experiment set data frame for a given modality
Subset$byRowNames

Extract subset of columns from a data frame or a list of data frames
plot.Corr

Plot the density distributions for correlation object(s)
corr.boxplot.JointUniquePairs

Boxplot of correlations by match group
Display$copy

Save current plot to the file
Display$create

Open a new display device
getDiff.JointIdMap

Create an IdMapDiff object
DataFilter$fisherTransformJacobean

Compute the Fisher transform Jacobean
Misc$CsvList.merge

Pairwise merge of two string vectors
Misc

The Misc class
getCounts.IdMap

Compute the count of secondaryIDs for each primary ID
interactive.corr.plot.JointUniquePairs

Interactive plot of correlation densities
JointIdMap

The Joint ID Map class
CorrData$pack.experiments

Convert aligned experiment data into the data structure incapsulated within the CorrData object
as.data.frame.IdMapBase

Retrieves a data frame encapsulated within the given IdMapBase object
DataFilter$fisherTransformInverse

Compute the Fisher inversed transform
DataFilter

The DataFilter class
[.IdMapBase

Access the elements of a data frame encapsulated within the given IdMapBase object using indexation
JointUniquePairs

The JointUniquePairs class
as.MultiSet.CorrData

Convert CorrData object into MultiSet object
Mixture

The Mixture class
plot.IdMapDiffCounts

Produce a fountain plot representing the quantitative relationship of the compound events
Subset$byColNames

Extract subset of columns from a data frame or a list of data frames
JointUniquePairs$boxplotdataJitter

Plot a set of points representing the density distribution of a data set
getCompoundEvents.IdMapDiffCounts

Get compound events
subsetCorr.JointUniquePairs

Subset the Corr object
plot.Mixture

Plot the results of mixture modeling
plot.IdMapCounts

Compute and plot the (inversed) ecdf for each ID Map count entry within the IdMapCounts object
UniquePairs$create

Create a UniquePairs object from a single IdMap or a list of IdMap objects
Subset$byColumn

# Extract subset of rows from a data frame or a list of data frames by intersecting on a particular column
aligned.IdMapBase

Checks if two IdMapBase objects match on column names and primary ID set
getMapNames.JointUniquePairs

Get the names of UniquePairs objects encapsulated within the given JointUniquePairs object
Misc$interleave

Interleave two matrixes by columns
interactive.corr.boxplot.JointUniquePairs

Interactive boxplot of correlations by match group
interactive.mixture.plot.JointUniquePairs

Interactive plot of mixture model components
Misc$to.index.expr

Convert expression into index expression for a given list or data frame object
secondaryKey.IdMapBase

Retrieves a secondary key for a given IdMapBase object
primaryKey.Mixture

Retrieves a primary key for a given Mixture object
Display$textBoundingBox

Determine the size of the text bounding box
subsetData.JointUniquePairs

Subset data on a UniquePairsMatch object
Display$zoom.pars

Zoom graphics parameters