mergeFunc: Funtion to merge states based on their state means

In aCGH: Classes and functions for Array Comparative Genomic Hybridization data

Description

mergeFunc takes the output of hmm.run.func (or find.hmm.states) with a particular model selection criterion and iteratively merges the states with means closer than a supplied threshold. mergeHmmStates is a frontend for mergeFunc using aCGH object.

Usage

mergeHmmStates(aCGH.obj, model.use = 1, minDiff = 0.25)
mergeFunc(statesres, minDiff = 0.1)

Arguments

aCGH.obj	Object of class aCGH.
statesres	the sublist of the states.hmm list output from find.hmm.states for a given model selection crterion
minDiff	The states whose predicted values are less than minDiff apart are merged into one state and all the predicited values are recomputed.
model.use	Model selection criterion to use, See find.hmm.states.

Details

This function is intended to reduce effect of the possible small magnitude technological artifacts on the structure determination.

Value

List containing states.hmm object is returned.

Author(s)

Jane Fridlyand

References

Application of Hidden Markov Models to the analysis of the array CGH data, Fridlyand et.al., JMVA, 2004

See Also

aCGH, find.hmm.states

aCGH documentation built on Nov. 8, 2020, 6:58 p.m.