cghseg (version 1.0.5)

CGHdata-class: Class "CGHdata"

Description

The CGHdata class is built to store the dataset

Objects from the Class

Objects can be created by calls of the form new("CGHdata", Y).

Y:

dataframe containing recorded values. One column per profile (of the same length), with patient IDs as column names. If the data contains probeID, then one column of Y must be named probeID. If the data contains the genomic position, then one column of Y must be named genomic.position. If the data contains GC content of the probe then one column of Y must be named GCcontent.

The dataset is checked while constructing the class. If colnames are not GCcontent, genomic.position, probeID, all columns will be considered as microarray signals.

Slots

Y:

Contains the data one field per patient (list)

probeID:

Contains the ID of each probe (factor)

genomic.position:

Contains the genomic position of each probe (numeric)

GCcontent:

Contains the GC content of each probe (numeric)

Methods

[

Accessor to slots of the class

initialize

to construct the class

getuniKmax

Assesses the maximum number of segments per profile

getmultiKmax

Assesses the maximum total number of segments

multiseg

Joint segmentation of multiple CGH profiles

uniseg

Separate segmentation single CGH profiles

print

print class object

show

show class object

summary

summary of class object

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)
#show(CGHd)
#summary(CGHd)
# }