TRONCO, a package for TRanslational ONCOlogy


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Documentation for package ‘TRONCO’ version 1.0.0

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confidence provides various kinds of confidence measures for an inferred progression model
confidence.conditional provides various kinds of confidence measures for an inferred progression model
confidence.data.conditional provides various kinds of confidence measures for an inferred progression model
confidence.data.joint provides various kinds of confidence measures for an inferred progression model
confidence.data.single provides various kinds of confidence measures for an inferred progression model
confidence.fit.conditional provides various kinds of confidence measures for an inferred progression model
confidence.fit.joint provides various kinds of confidence measures for an inferred progression model
confidence.fit.single provides various kinds of confidence measures for an inferred progression model
confidence.joint provides various kinds of confidence measures for an inferred progression model
confidence.single provides various kinds of confidence measures for an inferred progression model
data.load load a dataset (binary matrix) from a file or a preloaded dataset.
events Events collection for Ovarian cancer CGH data
events.add add a new event (e.g., a missense point mutation for EGFR)
events.load load a set of events from file
ov.cgh Ovarian cancer CGH data
reset reset
reset.events reset
reset.types reset
tronco.bootstrap perform bootstrap algorithm
tronco.bootstrap.show show bootstrapping results
tronco.caprese runs CAPRESE algorithm
tronco.plot plot a progression model
types Types collection for Ovarian cancer CGH data
types.add add a new type of event (e.g., missense point mutation)
types.load load a set of types from file