cghseg (version 1.0.5)

getmultiKmax: Determining the maximum number of segments for joint segmentation

Description

Determining the total maximum number of segments according to the maximum number of segments for each profile

Usage

getmultiKmax(.Object,CGHo,uniKmax=NULL,multiKmax=NULL)

Arguments

.Object

an object of the CGHdata class

CGHo

an object of the CGHoptions class

uniKmax

NULL if no value is proposed, list of Kmax for each profile

multiKmax

NULL or a proposed value for multiKmax, to check validity

Value

multiKmax

total number of segments for joint segmentation

Details

CGHo["beta"] sets the proportion of each Kmax in multiKmax. If uniKmax[[i]] is the Kmax of profile i then $$\code{multiKmax} = \beta \times \sum_i \code{uniKmax[[i]]}$$ MultiKmax must be greater than the number of profiles, but should not be too small since it should be greater than the selected number of segments (unknown).

References

Joint segmentation, calling and normalization of multiple CGH profiles, Biostatistics (2011)

Examples

# NOT RUN {
set.seed(1)
simul   = simulprofiles(M=5,n=100,k.mean=2,SNR=5,lambda=1)
CGHd    = new("CGHdata",Y=simul$Y)
CGHo    = new("CGHoptions")

## Default initialization

multiKmax = getmultiKmax(CGHd,CGHo)

## Modification of all fields:
## to set multiKmax to 50% of the sum of Kmax of each profile:

beta(CGHo) = 0.5
multiKmax = getmultiKmax(CGHd,CGHo)

## Modification of uniKmax

uniKmax      = getuniKmax(CGHd,CGHo)
uniKmax[[1]] = 80
multiKmax    = getmultiKmax(CGHd,CGHo,uniKmax)

## Modification of uniKmax and multiKmax
## and check that the value is correct wrt options

uniKmax[[1]] = 80
multiKmax    = getmultiKmax(CGHd,CGHo,uniKmax,multiKmax = 10)
# }