Package: NAM 1.8.0

NAM: Nested Association Mapping

Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. 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.

Authors:Alencar Xavier [aut, cre], William Muir [aut], Katy Rainey [aut], Shizhong Xu [aut]

NAM_1.8.0.tar.gz
NAM_1.8.0.zip(r-4.7)NAM_1.8.0.zip(r-4.6)NAM_1.8.0.zip(r-4.5)
NAM_1.8.0.tgz(r-4.6-x86_64)NAM_1.8.0.tgz(r-4.6-arm64)NAM_1.8.0.tgz(r-4.5-x86_64)NAM_1.8.0.tgz(r-4.5-arm64)
NAM_1.8.0.tar.gz(r-4.7-arm64)NAM_1.8.0.tar.gz(r-4.7-x86_64)NAM_1.8.0.tar.gz(r-4.6-arm64)NAM_1.8.0.tar.gz(r-4.6-x86_64)
NAM_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
NAM/json (API)

# Install 'NAM' in R:
install.packages('NAM', repos = c('https://alenxav.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alenxav/nam/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • chr - Tetra-seed Pods
  • fam - Tetra-seed Pods
  • gen - Tetra-seed Pods
  • Gen - Multi-environmental trial
  • Obs - Multi-environmental trial
  • simu - Pseudo-Expectation Gauss-Seidel for Multivariate Models
  • X - Pseudo-Expectation Gauss-Seidel for Multivariate Models
  • y - Tetra-seed Pods
  • Y - Pseudo-Expectation Gauss-Seidel for Multivariate Models

On CRAN:

Conda:

openblascpp

5.80 score 2 stars 1 packages 52 scripts 333 downloads 18 mentions 76 exports 1 dependencies

Last updated from:cc936ca82f. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK157
linux-devel-x86_64OK142
source / vignettesOK208
linux-release-arm64OK149
linux-release-x86_64OK135
macos-release-arm64OK135
macos-release-x86_64OK196
macos-oldrel-arm64OK120
macos-oldrel-x86_64OK282
windows-develOK128
windows-releaseOK123
windows-oldrelOK130
wasm-releaseOK109

Exports:BCpibenBRR2calcSizecleanREPCNTcovareigXemBAemBBemBCemBDemBLemCVemDEemENemGWAemMLemML2emMXemRRFstfunIfunXG2A_KernelsGAUGdistgibbsgibbs2gmmGRMgsgwasgwas2gwas3gwasGEIMPImport_datainputRowKMUPKMUP2LDmarkovMCremlmeta3mkrmkr2Xmlmrrmrr2XmrrFastmrrV2MSXNNcovNNsrcNORPedMatPedMat2pegsPEGS_lapackplot.fstplot.gibbsplot.H2plot.NAMpressreferenceremlSAMPSAMP2snpH2snpQCSPCSPMtimesMatrixtimesVecwgr

Dependencies:Rcpp

Meta-analysis

Alencar Xavier and Shizhong Xu

Rendered fromvignette2.Rmdusingknitr::rmarkdownon May 23 2026.

Last update: 2018-09-12
Started: 2017-10-27

Introduction to NAM

Alencar Xavier ([email protected])

Rendered fromvignette1.Rmdusingknitr::rmarkdownon May 23 2026.

Last update: 2019-09-23
Started: 2017-10-27

Readme and manuals

Help Manual

Help pageTopics
Nested Association MappingNAM-package NAM
Tetra-seed Podschr fam gen tpod y
Multi-environmental trialGen met Obs
Fixation IndexFst plot.fst
Empirical Bayes Genome Wide Association Mappinggwas gwas2 gwas3 gwasGE meta3
Genome-wide predictionben wgr
Manhattan plot for Association Studiesplot.NAM
Bayesian Mixed Modelgibbs gibbs2 ml plot.gibbs
Pseudo-Expectation Gauss-Seidel for Multivariate Modelspegs PEGS_lapack simu X Y
Restricted Maximum LikelihoodMCreml reml
Genomic mixed modelgmm
Internal functionsBCpi BRR2 calcSize CNT covar eigX emBA emBB emBC emBD emBL emCV emDE emEN emGWA emML emML2 emMX emRR funI funX G2A_Kernels GAU Gdist GRM gs IMP Import_data inputRow KMUP KMUP2 LD markov mkr mkr2X mrr mrr2X mrrFast mrrV2 MSX NNcov NNsrc NOR PedMat PedMat2 press RcppExports SAMP SAMP2 SPC SPM timesMatrix timesVec
SNP heritabilityplot.H2 snpH2
SNP Quality ControlcleanREP reference snpQC