findAmplif.func
From aCGH v1.50.0
by Peter Dimitrov
Function to determine high level amplifications
This function identifies high level amplifications by considering the height, the width of an amplicon relative to the urrounding clones. Only narrow peaks much higher than its neigbors are considered as high level amplifications.
- Keywords
- models
Usage
findAmplif.func(absValSingle = 1, absValRegion = 1.5, diffVal1 = 1,
diffVal2 = 0.5, maxSize = 10000, translen.matr, trans.matr, aber,
outliers, pred, pred.obs, statesres)Arguments
- absValSingle
- A clone is declared to be an amplification if it is a focal aberration or an outlier and its value exceeds absValSingle
- absValRegion
- A clone is an amplification if if a clone belong to a region with width less than maxSize and observed value for a clones is greater than absValRegion
- diffVal1
- Clone is an amplification if it is an aberration and greater by diffVal1 than max of the two surrounding stretches
- diffVal2
- Clone is an amplification if it is an outlier, its observed values is greater by diffVal2 than max of the two surrounding stretches
- maxSize
- The clones may not be declared as amplifications if they belong to the states with spanning more than maxSize
- translen.matr
- State length matrix. The output of the
findTrans.func - trans.matr
- Transition matrix. The output of the
findTrans.func - aber
- Aberration matrix. The output of the
findAber.func - outliers
- Outliers matrix. The output of the
findOutliers.func - pred
- Predicted values matrix. The output of the
findOutliers.func - pred.obs
- Predicted values matrix with observed values assigned
to the outliers. The output of the
findOutliers.func - statesres
- The states output of the
hmm.run.func
Details
Note that all the distances are in Megabases and all the heights are on log2ratio scale.
Value
- amplif.matrix
- Binary matrix with a row for each clone and column for each sample. "1" indicates amplification ...
References
Application of Hidden Markov Models to the analysis of the array CGH data, Fridlyand et.al., JMVA, 2004
See Also
Community examples
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