runGLAD {snapCGH}R Documentation

Results of segmenting an aCGHList data object using the GLAD library

Description

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.

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

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
...

Details

For a detailed explanation of the GLAD algorithm please see the relevant section of the GLAD manual: glad

Value

The function returns an object of class SegList

See Also

glad MAList runHomHMM runDNAcopy SegList


[Package snapCGH version 1.4.0 Index]