Usage
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, ...)
Arguments
smoothfunc
Type of algorithm used to smooth LogRatio by a
piecewise constant function. Choose either lawsglad, aws::aws
or aws::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::aws function or shape of aws::laws.
If NULL, sigma is calculated from the data.
bandwidth
Set the maximal bandwidth hmax in the
aws::aws or aws::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 ($\lambda'$) used during the
Optimization of the number of breakpoints step.
lambdacluster
Penalty term ($\lambda*$) used during the MSHR
clustering by chromosome step.
lambdaclusterGen
Penalty term ($\lambda*$) 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
Risk alpha used for the Outlier detection step.
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