PedCNV: An implementation for association analysis with CNV data.

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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.

Author
Meiling Liu, Sungho Won and Weicheng Zhu
Date of publication
2014-01-02 19:18:18
Maintainer
Meiling Liu <meiling.sta@gmail.com>
License
MIT + file LICENSE
Version
0.1
URLs

View on CRAN

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

Files in this package

PedCNV
PedCNV/src
PedCNV/src/Makevars
PedCNV/src/algorithm.cpp
PedCNV/src/Makevars.win
PedCNV/src/silWidth.cpp
PedCNV/src/getInitial.cpp
PedCNV/NAMESPACE
PedCNV/data
PedCNV/data/signal.RData
PedCNV/data/fam.RData
PedCNV/data/phi.RData
PedCNV/data/envirX.RData
PedCNV/R
PedCNV/R/silWidth.R
PedCNV/R/docs.R
PedCNV/R/AssoTestProcCS_mix.R
PedCNV/R/ClusProc.R
PedCNV/R/score_test.R
PedCNV/R/cnvlmm_plot.R
PedCNV/R/AI_EM_mixed.R
PedCNV/MD5
PedCNV/DESCRIPTION
PedCNV/man
PedCNV/man/print.clust.Rd
PedCNV/man/envirX.Rd
PedCNV/man/STE.Rd
PedCNV/man/PedCNV-package.Rd
PedCNV/man/AssoTestProc.Rd
PedCNV/man/fam.Rd
PedCNV/man/STIM.Rd
PedCNV/man/phi.Rd
PedCNV/man/print.asso.Rd
PedCNV/man/signal.Rd
PedCNV/man/plot.clust.Rd
PedCNV/man/ClusProc.Rd
PedCNV/LICENSE