IdMappingAnalysis (version 1.16.0)

getCompoundEvents.IdMapDiffCounts: Get compound events

Description

Transforms the IdMapDiffCounts triplet into the form suitable for using within the fountain plot. Computed on the fly within the IdMapDiffCounts$summary() and IdMapDiffCounts$plot() functions.

Usage

"getCompoundEvents"(this, verbose=FALSE, ...)

Arguments

verbose

If TRUE enables diagnostic messages. Default is FALSE.

...

Not used

Value

A data.frame with 7 columns each corresponding to a particular compaund set derived from the event triplet and with rows containing mathches (TRUE or FALSE) for a given primary ID. The columns and the compaund set description are as follows:

excess.both

A and B have non-empty intersection and both sets have unique elements

excess.left

A and B have non-empty intersection and only A has unique elements

excess.right

A and B have non-empty intersection and only B has unique elements

same.list

Non-empty A and B are the same

in.left.only

Only A set is non-empty

in.right.only

Only B set is non-empty

in.neither

Both sets are empty

See Also

For more information see IdMapDiffCounts.

Examples

 #create IdMapDiffCounts object
 IDs<-IdMapBase$primaryIDs(examples$msmsExperimentSet);
 jointIdMap<-JointIdMap(examples$identDfList,primaryIDs=IDs);
 diffs<-jointIdMap$getDiff("NetAffx_F","DAVID_Q",verbose=TRUE);
 diffCounts<-IdMapDiffCounts(diffs);

 # get compound events
 events<-diffCounts$getCompoundEvents();
 events[1:10,];