Package: NAM 1.7.4

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, William Muir, Katy Rainey, Shizhong Xu.

NAM_1.7.4.tar.gz
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NAM.pdf |NAM.html✨
NAM/json (API)

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

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • Gen - Multi-environmental trial
  • Obs - Multi-environmental trial
  • chr - Tetra-seed Pods
  • fam - Tetra-seed Pods
  • gen - Tetra-seed Pods
  • y - Tetra-seed Pods

On CRAN:

59 exports 2 stars 3.30 score 1 dependencies 1 dependents 18 mentions 44 scripts 477 downloads

Last updated 5 years agofrom:842fbe75f0. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 05 2024
R-4.5-win-x86_64NOTESep 05 2024
R-4.5-linux-x86_64NOTESep 05 2024
R-4.4-win-x86_64NOTESep 05 2024
R-4.4-mac-x86_64NOTESep 05 2024
R-4.4-mac-aarch64NOTESep 05 2024
R-4.3-win-x86_64NOTESep 05 2024
R-4.3-mac-x86_64NOTESep 05 2024
R-4.3-mac-aarch64NOTESep 05 2024

Exports:bencalcSizecleanREPCNTcovareigXemBAemBBemBCemBLemCVemDEemENemRRFstfunIfunXG2A_KernelsGAUGdistgibbsgibbs2gmmgsgwasgwas2gwas3gwasGEIMPImport_datainputRowKMUPKMUP2LDmarkovMCremlmeta3mlMSXNNcovNNsrcNORPedMatPedMat2plot.fstplot.gibbsplot.H2plot.NAMpressreferenceremlSAMPSAMP2snpH2snpQCSPCtimesMatrixtimesVecwgr

Dependencies:Rcpp

Meta-analysis

Alencar Xavier and Shizhong Xu

Rendered fromvignette2.Rmdusingknitr::rmarkdownon Sep 05 2024.

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

Introduction to NAM

Alencar Xavier ([email protected])

Rendered fromvignette1.Rmdusingknitr::rmarkdownon Sep 05 2024.

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
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