find.genomic.events {aCGH}  R Documentation 
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.
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)
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 least medChrom.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 least medChrom.min has to be
greater or less than 0.

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.
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 .

aCGH
find.hmm.states
mergeFunc
findAber.func
findTrans.func
findAmplif.func
findOutliers.func