runGLAD {snapCGH} | R Documentation |
This function allows the detection of breakpoints in genomic profiles
obtained by array CGH technology and affects a status (gain, normal
or lost) to each clone. It requires that the library GLAD
is loaded.
runGLAD(input, smoothfunc="lawsglad", base=FALSE, sigma = NULL, bandwidth=10, round=2, lambdabreak=8, lambdacluster=8, lambdaclusterGen=40, type="tricubic", param=c(d=6), alpha=0.001, method="centroid", nmax=8, verbose=FALSE, ...)
input |
An object of class MAList or SegList |
smoothfunc |
Type of algorithm used to smooth LogRatio by a
piecewise constant function. Choose either lawsglad , aws or
laws . |
base |
If TRUE , the position of clone is the physical position onto
the chromosome, otherwise the rank position is used. |
sigma |
Value to be passed to either argument sigma2
of aws function or shape of
laws . If NULL , sigma is calculated from
the data. |
bandwidth |
Set the maximal bandwidth hmax in the
aws or laws function. For
example, if bandwidth=10 then the hmax value is set
to 10*X_N where X_N is the position of the last clone. |
round |
The smoothing results are rounded or not depending on
the round argument. The round value is passed to the
argument digits of the round function. |
lambdabreak |
Penalty term (λ') used during the Optimization of the number of breakpoints step. |
lambdacluster |
Penalty term (λ*) used during the MSHR clustering by chromosome step. |
lambdaclusterGen |
Penalty term (λ*) used during the HCSR clustering throughout the genome step. |
type |
Type of kernel function used in the penalty term during the Optimization of the number of breakpoints step, the MSHR clustering by chromosome step and the HCSR clustering throughout the genome step. |
param |
Parameter of kernel used in the penalty term. |
alpha |
Parameter for ?????. |
method |
The agglomeration method to be used during the MSHR clustering by chromosome and the HCSR clustering throughout the genome clustering steps. |
nmax |
Maximum number of clusters (N*max) allowed during the the MSHR clustering by chromosome and the HCSR clustering throughout the genome clustering steps. |
verbose |
If TRUE some information are printed |
... |
For a detailed explanation of the GLAD algorithm please see the
relevant section of the GLAD manual: glad
The function returns an object of class SegList
glad
MAList
runHomHMM
runDNAcopy
SegList