Description Usage Arguments Details Value Author(s) References See Also

`mergeStates`

takes the output of a segmentation algorithm in
the form of a `SegList`

and iteratively merges the
states with means closer than a supplied threshold.

1 | ```
mergeStates(segList, MergeType = 1, pv.thres=0.0001, ansari.sign=0.01, minDiff = 0.25)
``` |

`segList` |
Object of class |

`MergeType` |
Select either 1 or 2. 1 uses a new merging algorithm developed by Hanni Willenbrock and Jane Fridlyand. |

`pv.thres` |
Significance threshold for Wilcoxon test for level merging. Used when MergeType = 1. |

`ansari.sign` |
Significance threshold for Ansari-Bradley test. Used when MergeType = 1. |

`minDiff` |
The states whose predicted values are less than minDiff apart are merged into one state and all the predicted values are recomputed. Used when MergeType = 2. |

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

A `SegList`

object is returned with the merged states
stored in the `pred`

list.

Jane Fridlyand

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

`SegList`

,
`runHomHMM`

,
`runGLAD`

,
`runDNAcopy`

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