cpgen: Parallelized Genomic Prediction and GWAS

Share:

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.

Author
Claas Heuer
Date of publication
2015-09-15 08:35:30
Maintainer
Claas Heuer <cheuer@tierzucht.uni-kiel.de>
License
GPL (>= 2)
Version
0.1
URLs

View on CRAN

Man pages

ccolmv
Colwise means or variances
ccov
ccov
ccross
ccross
cCV
Generate phenotype vectors for cross validation
cGBLUP
Genomic BLUP
cgrm
Genomic Relationship Matrices
cgrm.A
Additive Genomic Relationship Matrix
cgrm.D
Dominance Genomic Relationship Matrix
cGWAS
Genomewide Association Study
cGWAS.emmax
Genomewide Association Study - EMMAX
check_openmp
Check OpenMP-support.
clmm
Linear Mixed Models using Gibbs Sampling
cmaf
cmaf
cpgen-package
cpgen - Parallel genomic evaluations
cpgen-parallel
Multithreading using 'cpgen'
cpowop
Square matrix power operator
crossprodop
(Parallel) Matrix product operator
cscale_inplace
cscale_inplace
cscanx
Read in a matrix from a file
csolve
csolve
cSSBR
Single Step Bayesian Regression
cSSBR.setup
Preparing Model terms for Single Step Bayesian Regression
get_cor
Compute the prediction accuracy from Cross Validition
get_max_threads
Get the maximum number of threads available
get_num_threads
Get the number of threads for 'cpgen'
get_pred
Extract predictions vectors of an object returned by 'clmm'...
rand_data
Generate random data for test purposes
set_num_threads
Set the number of OpenMP threads used by the functions of...

Files in this package

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