transformAndWritePoset: Transforms poset

In cbg-ethz/pathTiMEx: Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics

Description

transformAndWritePoset transforms the existing optimal poset from the previous optimization step to a new compatible poset, to be used as starting solution by the next run of H-CBN.

Usage

transformAndWritePoset(path, name, oldStruct, newPathMat)

Arguments

path	path where the new compatible poset is written
name	name of the poset file to be written
oldStruct	the old poset to be transformed, encoding order relations between pathways at the previous optimization step
newPathMat	current binary alteration matrix at the level of pathways, with rows representing samples and columns pathways, where an 1 represents that a pathway is altered in a sample

Details

The role of this function is to create a compatible starting poset for the new H-CBN optimization step, on the basis of the current optimal poset. This is done by simply removing any edge from between events which do not longer exist as pathways. The numbering of the evnets is kept as in the current poset, without checking for consistency between pathways between the old and current groupings. The new poset is written to the file path/name.poset.

Value

nothing

Author(s)

Simona Constantinescu, [e-mail]

cbg-ethz/pathTiMEx documentation built on May 13, 2019, 2:03 p.m.