# findAmplif.func

0th

Percentile

##### 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

aCGH