NAM: Nested Association Mapping

Designed for association studies in nested association mapping (NAM) panels, also handling experimental and random panels. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.

Author
Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Date of publication
2016-10-20 23:14:00
Maintainer
Alencar Xavier <alenxav@gmail.com>
License
GPL-3
Version
1.5.0

View on CRAN

Man pages

cleanREP
Manage Duplicated Genotypes
Fst
Fixation Index
gibbs
Bayesian Mixed Model
gmm
Genomic mixed model
gwas
Empirical Bayes Genome Wide Association Mapping
Internals
Internal functions
Manhattan
Manhattan plot for Association Studies
met
Multi-environmental trial
NAM-package
Nested Association Mapping
reference
Changing the Reference Genotype
reml
Restricted Maximum Likelihood
snpH2
SNP heritability
snpQC
SNP Quality Control
tpod
Tetra-seed Pods
wgr
Whole-genome Regression

Files in this package

NAM
NAM/inst
NAM/inst/CITATION
NAM/inst/add
NAM/inst/add/Ggamma.R
NAM/inst/add/gwasPAR.R
NAM/inst/add/fastPhase.R
NAM/inst/add/cvNAM.R
NAM/inst/add/modelSelect.R
NAM/inst/add/sparseGMM.R
NAM/inst/doc
NAM/inst/doc/gwa_ge_interactions.pdf
NAM/inst/doc/vignette2.html
NAM/inst/doc/vignette1.Rmd
NAM/inst/doc/background_stat_gen.pdf
NAM/inst/doc/vignette2.Rmd
NAM/inst/doc/vignette1.html
NAM/inst/doc/vignette2.R
NAM/inst/doc/gwa_description.pdf
NAM/src
NAM/src/SAMP.cpp
NAM/src/emBB.cpp
NAM/src/timesMatrix.cpp
NAM/src/emBA.cpp
NAM/src/timesVec.cpp
NAM/src/funI.cpp
NAM/src/funX.cpp
NAM/src/emRR.cpp
NAM/src/emBL.cpp
NAM/src/emBC.cpp
NAM/src/gs.cpp
NAM/src/KMUP.cpp
NAM/src/KMUP2.cpp
NAM/src/SAMP2.cpp
NAM/src/inputRow.cpp
NAM/src/RcppExports.cpp
NAM/src/calcSize.cpp
NAM/NAMESPACE
NAM/demo
NAM/demo/fieldvar.R
NAM/demo/metaGxE.R
NAM/demo/fittingMET.R
NAM/demo/00Index
NAM/demo/metagwas.R
NAM/data
NAM/data/met.RData
NAM/data/tpod.RData
NAM/R
NAM/R/gmm.R
NAM/R/wgr.R
NAM/R/gwas.R
NAM/R/gibbs.R
NAM/R/RcppExports.R
NAM/R/reml.R
NAM/R/snp.R
NAM/vignettes
NAM/vignettes/vignette1.Rmd
NAM/vignettes/vignette2.Rmd
NAM/MD5
NAM/build
NAM/build/vignette.rds
NAM/DESCRIPTION
NAM/man
NAM/man/reference.Rd
NAM/man/gmm.Rd
NAM/man/wgr.Rd
NAM/man/reml.Rd
NAM/man/cleanREP.Rd
NAM/man/gwas.Rd
NAM/man/snpH2.Rd
NAM/man/gibbs.Rd
NAM/man/snpQC.Rd
NAM/man/tpod.Rd
NAM/man/NAM-package.Rd
NAM/man/Manhattan.Rd
NAM/man/met.Rd
NAM/man/Fst.Rd
NAM/man/Internals.Rd