getmultiKmax: Determining the maximum number of segments for joint...
In cghseg: Segmentation Methods for Array CGH Analysis

Description Usage Arguments Details Value Author(s) References Examples

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

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

`.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

CGHo["beta"] sets the proportion of each Kmax in multiKmax. If uniKmax[[i]] is the Kmax of profile i then

\code{multiKmax} = β \times ∑_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).

multiKmax

total number of segments for joint segmentation

F. Picard, E. Lebarbier, M. Hoebeke, G. Rigaill, B. Thiam, S. Robin

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

#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)