PedCNV: An implementation for association analysis with CNV data.
Version 0.1

An implementation for association analysis with CNV data in R. It provides two methods for association study: first, the observed probe intensity measurement can be directly used to detect the association of CNV with phenotypes of interest. Second, the most probable copy number is estimated with the proposed likelihood and the association of the most probable copy number with phenotype is tested. This method can be applied to both the independent and correlated population.

AuthorMeiling Liu, Sungho Won and Weicheng Zhu
Date of publication2014-01-02 19:18:18
MaintainerMeiling Liu <meiling.sta@gmail.com>
LicenseMIT + file LICENSE
Version0.1
URL https://github.com/rksyouyou/PedCNV
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PedCNV")

Getting started

Package overview

Popular man pages

AssoTestProc: CNV association test procedure
envirX: CNV simulated environmental variables
fam: CNV simulated data
plot.clust: Plots clustering result
print.asso: Prints association study results
print.clust: Prints clustering results
STIM: Score test with the intensity value
See all...

All man pages Function index File listing

Man pages

AssoTestProc: CNV association test procedure
ClusProc: CNV clustering Procedure
envirX: CNV simulated environmental variables
fam: CNV simulated data
PedCNV-package: CNV association implementation
phi: Empirical correlation matrix
plot.clust: Plots clustering result
print.asso: Prints association study results
print.clust: Prints clustering results
signal: CNV simulated intensity measurements
STE: Score test with the most probable CNV
STIM: Score test with the intensity value

Functions

AssoTestProc Man page Source code
CNVtypeAnay Source code
ClusProc Man page Source code
ClusProc0 Source code
Inde Source code
PedCNV-package Man page
STE Man page Source code
STIM Man page Source code
doAI_REML Source code
doEM_REML Source code
doPolyGenic Source code
envirX Man page
fam Man page
getInitial Source code
phi Man page
plot.clust Man page Source code
print.asso Man page Source code
print.clust Man page Source code
signal Man page
silWidth Source code

Files

src
src/Makevars
src/algorithm.cpp
src/Makevars.win
src/silWidth.cpp
src/getInitial.cpp
NAMESPACE
data
data/signal.RData
data/fam.RData
data/phi.RData
data/envirX.RData
R
R/silWidth.R
R/docs.R
R/AssoTestProcCS_mix.R
R/ClusProc.R
R/score_test.R
R/cnvlmm_plot.R
R/AI_EM_mixed.R
MD5
DESCRIPTION
man
man/print.clust.Rd
man/envirX.Rd
man/STE.Rd
man/PedCNV-package.Rd
man/AssoTestProc.Rd
man/fam.Rd
man/STIM.Rd
man/phi.Rd
man/print.asso.Rd
man/signal.Rd
man/plot.clust.Rd
man/ClusProc.Rd
LICENSE
PedCNV documentation built on May 19, 2017, 8:32 p.m.

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