cghseg (version 1.0.5)

CGHresults-class: Class "CGHresults"

Description

The CGHresults class is built to store the results of cghseg.

Objects from the Class

Objects can be created by calls of the form new("CGHresults", CGHd, CGHo).

Slots

mu:

list of dataframes containing the position of breakpoints and estimated means (list)

theta:

List of effects used for normalization : waveffect, GCeffect (listOrNULL)

loglik:

Log-likelihood of the selected model (numeric)

nbiter:

number of iterations (numeric)

from:

Name of the function that produced the results (character)

probeID:

Contains the ID of each probe (factor)

genomic.position:

Contains the genomic position of each probe (numeric)

options:

list of options (of class CGHoptions)

Methods

[

Accessor to slots of the class

initialize

to construct the class

summary

summary of CGHr

getbp

Extract the frequency of breakpoints

getsegprofiles

Extract model predictions

getlevels

Extract levels of segments

getbgoutliers

Identification of outliers in the background intensity

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")
CGHr           = multiseg(CGHd,CGHo)
bplist         = getbp(CGHr)
segprofiles    = getsegprofiles(CGHr)
# }