Description Usage Arguments Details Value Author(s) References Examples
Maximum number of segments per profile according to a given proportion of the length of the data using a univariate pre-segmentation.
1 | getuniKmax(.Object,CGHo,uniKmax=NULL)
|
.Object |
an object of the CGHdata class |
CGHo |
an object of the CGHoption class |
uniKmax |
NULL if no value is proposed, list of Kmax for each profile |
CGHo["alpha"]
sets the proportion of length of each profile
that will be used for pre-segmentation. If ni is the length of profile
i then the pre-segmentation is done using a Kmax=max(200,alpha n_i). Pre-segmentation is done to propose a number of segments Khi for
each profile i. Then the maximum number of segments authorized per
profile will be 2*Khi. The speed of execution of the method decreases
with Kmax. Each Kmax must fulfill some conditions wrt CGHo
:
\code{uniKmax[[i]]} > \code{nblevels}
\code{uniKmax[[i]]}< n_i
Tuning Khi for each profile is a way to reduce the complexity of the multisample segmentation.
uniKmax |
list containing the maximum number of segments per profile. If !is.null(uniKmax) in the entry of the method, the method checks its validity. |
F. Picard, E. Lebarbier, M. Hoebeke, G. Rigaill, B. Thiam, S. Robin
Joint segmentation, calling and normalization of multiple CGH profiles, Biostatistics (2011)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | #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
#uniKmax = getuniKmax(CGHd,CGHo)
## Modification of all fields:
## to tune uniKmax using to 50% of the length of each profile :
## this may provide the same result since a model selection is performed
## for tuning.
#alpha(CGHo) = 0.5
#uniKmax = getuniKmax(CGHd,CGHo)
## Modification of one field for one profile
## and check that the value is correct wrt options
#uniKmax[[1]] = 80
#uniKmax = getuniKmax(CGHd,CGHo,uniKmax)
|
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