mergeStates

MergeLevels.new

MergeLevels.old

combine.func


    Object of class <code><a rd-options="snapCGH:SegList" href="/link/SegList?package=snapCGH&version=1.42.0&to=snapCGH%3ASegList" data-mini-rdoc="snapCGH:SegList::SegList">SegList</a></code>.
  

segList


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

MergeType

Significance threshold for Wilcoxon test for
    level merging.  Used when MergeType = 1.

pv.thres

Significance threshold for Ansari-Bradley test. Used when MergeType = 1.

ansari.sign

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.   
  

minDiff


  <code>mergeStates</code> takes the output of a segmentation algorithm in
  the form of a <code><a rd-options="snapCGH:SegList" href="/link/SegList?package=snapCGH&version=1.42.0&to=snapCGH%3ASegList" data-mini-rdoc="snapCGH:SegList::SegList">SegList</a></code> and iteratively merges the
  states with means closer than a supplied threshold.


models

Methods for segmenting, normalising and processing aCGH
data; including plotting functions for visualising raw and
segmented data for individual and multiple arrays.

John Marioni

snapCGH

Segmentation, normalisation and processing of aCGH data.

mergeStates function

Object of class <code><a href="SegList" rd-options="snapCGH:SegList">SegList</a></code>.

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

Significance threshold for Wilcoxon test for
    level merging.  Used when MergeType = 1.

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.

<code>mergeStates</code> takes the output of a segmentation algorithm in
  the form of a <code><a href="SegList" rd-options="snapCGH:SegList">SegList</a></code> and iteratively merges the
  states with means closer than a supplied threshold.

mergeStates: Function to merge states based on their state means

Description

Usage

Arguments

Value

Details

References

See Also