find.genomic.events
Finds the genomic events associated with each of the array CGH samples
Finds the genomic events associated with each of the array CGH samples. Events include whole chromosomal gains and losses, aberrations, transitions, amplifications and their respective counts and sizes. The hmm states has to be computed before using this function.
 Keywords
 models
Usage
find.genomic.events(aCGH.obj, maxChrom = 23, factor = 5, maxClones = 1, maxLen = 1000, absValSingle = 1, absValRegion = 1, diffVal1 = 1, diffVal2 = .5, maxSize = 10000, pChrom.min = .9, medChrom.min = .1)
Arguments
 aCGH.obj

Object of class
aCGH
.  maxChrom
 Highest chromosomal number to find events.
 factor
 Determines outliers. See
findOutliers.func
.  maxClones
 Determines aberrations. See
findAber.func
.  maxLen
 Determines aberrations. See
findAber.func
.  absValSingle
 Determines amplifications. See
findAmplif.func
.  absValRegion
 Determines amplifications. See
findAmplif.func
.  diffVal1
 Determines amplifications. See
findAmplif.func
.  diffVal2
 Determines amplifications. See
findAmplif.func
.  maxSize
 Determines amplifications. See
findAmplif.func
.  pChrom.min

Determines whole chromosomal gains and losses. Chromosome should
contain no transitions, have its absolute median equal or greater
than
medChrom.min
and at leastmedChrom.min
has to be greater or less than 0.  medChrom.min

Determines whole chromosomal gains and losses. Chromosome should
contain no transitions, have its absolute median equal or greater
than
medChrom.min
and at leastmedChrom.min
has to be greater or less than 0.
Details
The default parameters generally work. Threshold for merging may be changed depending on the expected normal cell contamination and/or expected magnitude of the changes. AIC model generally works, however, may need to be readjusted depending on how liberal or conservative one wants to be in finding genomic events. We recommend BIC criterion with delta = 1 for noisier data.
Value
 num.transitions
 matrix of dimensions maxChrom by number of samples. It contains number of transitions that were recorded on a given chromosome for a given sample.
 num.amplifications
 matrix of dimensions maxChrom by number of samples It contains number of amplifications that were recorded on a given chromosome for a given sample.
 num.aberrations
 matrix of dimensions maxChrom by number of samples. It contains number of focal aberrations that were recorded on a given chromosome for a given sample.
 num.outliers
 matrix of dimensions maxChrom by number of samples. It contains number of outliers that were recorded on a given chromosome for a given sample.
 num.transitions.binary
 binary matrix of dimensions maxChrom by number of samples. Nonzero entry indicates whether 1 or more transitions were recorded on a given chromosome for a given sample.
 num.amplifications.binary
 binary matrix of dimensions maxChrom by number of samples. Nonzero entry indicates whether 1 or more amplifications were recorded on a given chromosome for a given sample.
 num.aberrations.binary
 binary matrix of dimensions maxChrom by number of samples. Nonzero entry indicates whether 1 or more focal aberrations were recorded on a given chromosome for a given sample.
 num.outliers.binary
 binary matrix of dimensions maxChrom by number of samples. Nonzero entry indicates whether 1 or more outliers were recorded on a given chromosome for a given sample.
 whole.chrom.gain.loss
 matrix of dimensions maxChrom by number of samples. Positive entry indicates that a given chromosome was gained in a given sample, negative entry indicates that a given chromosome was lost in a given sample, 0 entry is normal chromosome and NA marks chromosomes with one or more transition.
 size.amplicons
 matrix of dimensions maxChrom by number of samples. Reports size of a given chromosome that is amplified (kb units) in a given sample.
 num.amplicons
 matrix of dimensions maxChrom by number of samples. Reports number of disjoint amplicons on a given chromosome for a given sample.
 outliers

list containing 3 matrices of dimensions number of clones by number
of samples. See
findOutliers.func
.  aberrations

list containing a matrix of dimensions number of clones by number
of samples. See
findAber.func
.  transitions

list containing 2 matrices of dimensions number of clones by number
of samples. See
findTrans.func
.  amplifications

list containing a matrix of dimensions number of clones by number
of samples. See
findAmplif.func
.
See Also
aCGH
find.hmm.states
mergeFunc
findAber.func
findTrans.func
findAmplif.func
findOutliers.func