Meta-analysis of multiple populations along with GxE | Genome-wide association | AMMI term | Hypothesis testing | Woodbury's matrix identities
This package is considered a duplicate. The official version of this package is found at:https://alenxav.r-universe.dev/NAM
Package: NAM 1.8.0
Alencar Xavier
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:
NAM_1.8.0.tar.gz
NAM_1.8.0.zip(r-4.7-x86_64)NAM_1.8.0.zip(r-4.7-arm64)NAM_1.8.0.zip(r-4.6-x86_64)NAM_1.8.0.zip(r-4.6-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✨
DESCRIPTION
card.svg |card.png
NAM/json (API)
| # Install 'NAM' in R: |
| install.packages('NAM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
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
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:e2980d8fc7. Checks:10 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 109 | ||
| linux-devel-x86_64 | OK | 567 | ||
| source / vignettes | OK | 193 | ||
| linux-release-arm64 | OK | 612 | ||
| linux-release-x86_64 | OK | 133 | ||
| windows-devel-arm64 | OK | 248 | ||
| windows-devel-x86_64 | OK | 135 | ||
| windows-release-arm64 | OK | 241 | ||
| windows-release-x86_64 | OK | 471 | ||
| wasm-release | OK | 103 |
Exports:BCpibenBRR2calcSizecleanREPCNTcovareigXemBAemBBemBCemBDemBLemCVemDEemENemGWAemMLemML2emMXemRRFstfunIfunXG2A_KernelsGAUGdistgibbsgibbs2gmmGRMgsgwasgwas2gwas3gwasGEIMPImport_datainputRowKMUPKMUP2LDmarkovMCremlmeta3mkrmkr2Xmlmrrmrr2XmrrFastmrrV2MSXNNcovNNsrcNORPedMatPedMat2pegsPEGS_lapackplot.fstplot.gibbsplot.H2plot.NAMpressreferenceremlSAMPSAMP2snpH2snpQCSPCSPMtimesMatrixtimesVecwgr
Dependencies:Rcpp
Meta-analysis
Last update: 2026-01-24
Started: 2016-01-29
Introduction to NAM
1. Installing the NAM package | 2. Loading and formatting data | 3. Genome-wide association studies | 4. Marker quality control | 5. Signatures of selection | 6. BLUPs and GEBVs | 7. Finding substructures | 8. Other structured populations | 9. Further background
Last update: 2026-01-24
Started: 2016-08-09
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Nested Association Mapping | NAM-package NAM |
| Tetra-seed Pods | chr fam gen tpod y |
| Multi-environmental trial | Gen met Obs |
| Fixation Index | Fst plot.fst |
| Empirical Bayes Genome Wide Association Mapping | gwas gwas2 gwas3 gwasGE meta3 |
| Genome-wide prediction | ben wgr |
| Manhattan plot for Association Studies | plot.NAM |
| Bayesian Mixed Model | gibbs gibbs2 ml plot.gibbs |
| Pseudo-Expectation Gauss-Seidel for Multivariate Models | pegs PEGS_lapack simu X Y |
| Restricted Maximum Likelihood | MCreml reml |
| Genomic mixed model | gmm |
| Internal functions | BCpi 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 heritability | plot.H2 snpH2 |
| SNP Quality Control | cleanREP reference snpQC |