cghseg (version 1.0.5)

CGHoptions-class: Class "CGHoptions"

Description

The CGHoptions class is built to store informations regarding the methods used in the cghseg package

Objects from the Class

Objects can be created by calls of the form new("CGHoptions").

Slots

select:

Model selection to select the number of segments; "mBIC","none" (character)

calling:

calling of segments (logical)

wavenorm:

Wave normalization; "none", "position", "spline" (character)

GCnorm:

GCcontent normalization; "none","linear" (character)

nblevels:

Number of levels when calling (numeric)

alpha:

Proportion of the individual signal length that gives uniKmax.

beta:

Proportion of the sum of uniKmax that gives multiKmax.

itermax:

Maximal number of iterations

nbprocs:

Number of available computer processes

Prototype

CGHo = new('CGHoptions') CGHo@select = "mBIC" CGHo@calling = FALSE CGHo@wavenorm = "position" CGHo@GCnorm = "none" CGHo@nblevels = 3 CGHo@alpha = 0.2 CGHo@beta = 0.5 CGHo@itermax = Inf CGHo@nbprocs = 1

Methods

[

Accessor to slots of the class

initialize

to construct the class

print

Print CGHo

show

Show CGHo

select<-

Modification of slot select; select(CGHo)<-

calling<-

Modification of slot calling; calling(CGHo)<-

wavenorm<-

Modification of slot wavenorm; wavenorm(CGHo)<-

GCnorm<-

Modification of slot GCnorm; GCnorm(CGHo)<-

nblevels<-

Modification of slot nblevels; nblevels(CGHo)<-

alpha<-

Modification of slot alpha; alpha(CGHo)<-

beta<-

Modification of slot beta; beta(CGHo)<-

itermax<-

Modification of slot itermax; itermax(CGHo)<-

nbprocs<-

Modification of slot nbproc; nbproc(CGHo)<-

References

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

Examples

# NOT RUN {
#CGHo = new("CGHoptions")
#showClass("CGHoptions")
# }