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cghseg (version 1.0.5)

Segmentation Methods for Array CGH Analysis

Description

Dedicated to the analysis of CGH (Comparative Genomic Hybridization) array profiles using segmentation models. 'cghseg' package is intended to detect breakpoints from CGH profiles. It can handle both single and multiple profiles analysis, to perform segmentation, normalization and calling. Methods for joint segmentation are described in : Picard and al. (2011), .

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Version

Install

install.packages('cghseg')

Monthly Downloads

54

Version

1.0.5

License

GPL (>= 2)

Maintainer

Samuel Blanck

Last Published

February 13th, 2020

Functions in cghseg (1.0.5)

alpha<-

Replace slot alpha
itermax<-

Replace slot itermax
multiseg

Joint segmentation of multiple CGH profiles
CGHoptions-class

Class "CGHoptions"
getbp

Breakpoints frequencies
CGHdata-class

Class "CGHdata"
nblevels<-

Replace slot nblevels
simulprofiles

simulprofiles
getlevels

Levels frequency
select<-

Replace slot select
CGHresults-class

Class "CGHresults"
calling<-

Replace slot calling
GCnorm<-

Replace slot GCnorm
getbgoutliers

getbgoutliers
getmultiKmax

Determining the maximum number of segments for joint segmentation
nbprocs<-

Replace slot nbprocs
segmeanCO

segmentation CGH profiles
getsegprofiles

getsegprofiles
wavenorm<-

Replace slot wavenorm
uniseg

Segmentation of univariate CGH profiles
beta<-

Replace slot beta
getuniKmax

Maximum number of segments per profile