cpgen: Parallelized Genomic Prediction and GWAS

Frequently used methods in genomic applications with emphasis on parallel computing (OpenMP). At its core, the package has a Gibbs Sampler that allows running univariate linear mixed models that have both, sparse and dense design matrices. The parallel sampling method in case of dense design matrices (e.g. Genotypes) allows running Ridge Regression or BayesA for a very large number of individuals. The Gibbs Sampler is capable of running Single Step Genomic Prediction models. In addition, the package offers parallelized functions for common tasks like genome-wide association studies and cross validation in a memory efficient way.

Install the latest version of this package by entering the following in R:
install.packages("cpgen")
AuthorClaas Heuer
Date of publication2015-09-15 08:35:30
MaintainerClaas Heuer <cheuer@tierzucht.uni-kiel.de>
LicenseGPL (>= 2)
Version0.1
https://github.com/cheuerde/cpgen

View on CRAN

Functions

\%**\% Man page
\%c\% Man page
ccolmv Man page
ccov Man page
ccross Man page
cCV Man page
cGBLUP Man page
cgrm Man page
cgrm.A Man page
cgrm.D Man page
cGWAS Man page
cGWAS.emmax Man page
check_openmp Man page
clmm Man page
cmaf Man page
cpgen-package Man page
cpgen-parallel Man page
cscale_inplace Man page
cscanx Man page
csolve Man page
cSSBR Man page
cSSBR.setup Man page
get_cor Man page
get_max_threads Man page
get_num_threads Man page
get_pred Man page
rand_data Man page
set_num_threads Man page

Files

src
src/Makevars
src/clmm.cpp
src/printer_unix.h
src/pedigree_stuff.h
src/printer.h
src/pedigree_stuff.c
src/ctools.h
src/cGWAS.cpp
src/actools.cpp
src/clmm
src/clmm/function_base.h
src/clmm/base_methods_abstract.h
src/clmm/mcmc.h
src/clmm/functions.h
src/clmm/mt_sampler.h
src/clmm/effects.h
src/clmm/R_sampler.h
src/clmm/mcmc_abstract.h
src/clmm/base_methods.h
src/clmm.h
src/Makevars.win
src/cGWAS.h
NAMESPACE
R
R/clmm.R R/cSSBR.R R/cGWAS.R R/ctools.R R/zzz.R
MD5
DESCRIPTION
man
man/cscale_inplace.Rd man/cpgen-package.Rd man/crossprodop.Rd man/cGWAS.emmax.Rd man/cmaf.Rd man/ccov.Rd man/set_num_threads.Rd man/ccross.Rd man/rand_data.Rd man/clmm.Rd man/cGBLUP.Rd man/cSSBR.Rd man/cpgen-parallel.Rd man/get_cor.Rd man/check_openmp.Rd man/csolve.Rd man/get_num_threads.Rd man/cscanx.Rd man/cCV.Rd man/cgrm.D.Rd man/cGWAS.Rd man/cgrm.Rd man/cSSBR.setup.Rd man/cgrm.A.Rd man/ccolmv.Rd man/get_pred.Rd man/cpowop.Rd man/get_max_threads.Rd

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