# Nested Association Mapping

## Documentation for package ‘NAM’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

NAM-package | Nested Association Mapping
BCpi | Internal functions
ben | Genome-wide prediction
BRR2 | Internal functions
calcSize | Internal functions
chr | Tetra-seed Pods
cleanREP | SNP Quality Control
CNT | Internal functions
covar | Internal functions
eigX | Internal functions
emBA | Internal functions
emBB | Internal functions
emBC | Internal functions
emBD | Internal functions
emBL | Internal functions
emCV | Internal functions
emDE | Internal functions
emEN | Internal functions
emGWA | Internal functions
emML | Internal functions
emML2 | Internal functions
emMX | Internal functions
emRR | Internal functions
fam | Tetra-seed Pods
Fst | Fixation Index
funI | Internal functions
funX | Internal functions
G2A_Kernels | Internal functions
GAU | Internal functions
Gdist | Internal functions
Gen | Multi-environmental trial
gen | Tetra-seed Pods
gibbs | Bayesian Mixed Model
gibbs2 | Bayesian Mixed Model
gmm | Genomic mixed model
GRM | Internal functions
gs | Internal functions
gwas | Empirical Bayes Genome Wide Association Mapping
gwas2 | Empirical Bayes Genome Wide Association Mapping
gwas3 | Empirical Bayes Genome Wide Association Mapping
gwasGE | Empirical Bayes Genome Wide Association Mapping
IMP | Internal functions
Import_data | Internal functions
inputRow | Internal functions
KMUP | Internal functions
KMUP2 | Internal functions
LD | Internal functions
markov | Internal functions
MCreml | Restricted Maximum Likelihood
met | Multi-environmental trial
meta3 | Empirical Bayes Genome Wide Association Mapping
mkr | Internal functions
mkr2X | Internal functions
ml | Bayesian Mixed Model
mrr | Internal functions
mrr2X | Internal functions
mrrFast | Internal functions
mrrV2 | Internal functions
MSX | Internal functions
NAM | Nested Association Mapping
NNcov | Internal functions
NNsrc | Internal functions
NOR | Internal functions
Obs | Multi-environmental trial
PedMat | Internal functions
PedMat2 | Internal functions
pegs | Pseudo-Expectation Gauss-Seidel for Multivariate Models
PEGS_lapack | Pseudo-Expectation Gauss-Seidel for Multivariate Models
plot.fst | Fixation Index
plot.gibbs | Bayesian Mixed Model
plot.H2 | SNP heritability
plot.NAM | Manhattan plot for Association Studies
press | Internal functions
RcppExports | Internal functions
reference | SNP Quality Control
reml | Restricted Maximum Likelihood
SAMP | Internal functions
SAMP2 | Internal functions
simu | Pseudo-Expectation Gauss-Seidel for Multivariate Models
snpH2 | SNP heritability
snpQC | SNP Quality Control
SPC | Internal functions
SPM | Internal functions
timesMatrix | Internal functions
timesVec | Internal functions
tpod | Tetra-seed Pods
wgr | Genome-wide prediction
X | Pseudo-Expectation Gauss-Seidel for Multivariate Models
Y | Pseudo-Expectation Gauss-Seidel for Multivariate Models
y | Tetra-seed Pods