computeSD.func
From aCGH v1.50.0
by Peter Dimitrov
Function to estimate experimental variability of a sample
This functions estimate experimental variability of a given sample. This value can be used to rank samples in terms of the quality as well as to derive thresholds for declaring gained and lost clones.
 Keywords
 models
Usage
computeSD.Samples(aCGH.obj, maxChrom = 22, maxmadUse = .3, maxmedUse = .5, maxState = 3, maxStateChange = 100,
minClone = 20)
computeSD.func(statesres, maxmadUse = 0.2, maxmedUse = 0.2, maxState = 3, maxStateChange = 100, minClone = 20, maxChrom = 22)
Arguments
 aCGH.obj

Object of class
aCGH
.  statesres
 The states.hmm object, generally is the output of
mergeFunc
.  maxmadUse
 Maximum median absolute deviation allowed to controbute to the overall variability calculation.
 maxmedUse
 Maximum median value for a state allowed to contribute to the calculation.
 maxState
 Maximum number of the states on a given chromosome for the states from that chromosome to be allowed to enter noise variability calculation.
 maxStateChange
 Maximum number of changes from state to state on a given chromosome for that chromosome to enter noise variability calculation.
 minClone
 Minimum number of clones in a state for clones in that sate to enter variability calculation.
 maxChrom
 Maxiumum chromosomal index (generally only autosomes are used for this calculation.
Details
Median absolute deviation is estimated in all the states passing the criteria defined by the parameters of the function. Then median of all MADs on individual chromosomes as well as across all chromosomes is taken to estimate chromosomal experimental variability and sample experimental variability.
Value
 madChrom
 Returns a matrix containing estimated variability for each chromosome for each sample.
 madGenome
 Returns a vector with estimate of experimental varibility for each sample.
References
Application of Hidden Markov Models to the analysis of the array CGH data, Fridlyand et.al., JMVA, 2004
See Also
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