AGT                     AGT data set
GRM                     Genetic Relationship Matrix
LCT                     LCT data set
LD                      Linkage Disequilibrium
LD.thin                 LD thinning
TTN                     TTN data set
as.bed.matrix           Creation of a bed.matrix
association.test        Association Test
bed.loadings            SNP loadings
bed.matrix-class        Class '"bed.matrix"'
gaston-package          gaston
lik.contour             Contour plot for two parameters likelihood
lmm.aireml              Linear mixed model fitting with AIREML
lmm.diago               Linear mixed model fitting with the
                        diagonalization trick
lmm.diago.likelihood    Likelihood of a linear mixed model
lmm.simu                Linear mixed model data simulation
logistic.mm.aireml      Logistic mixed model fitting with Penalized
                        Quasi-Likelihood / AIREML
random.pm               Random square definite positive matrix
read.bed.matrix         Read a 'bed.matrix'
read.vcf                Create a 'bed.matrix' from VCF files
reshape.GRM             Reshape a Genetic Relationship Matrix
score.fixed.linear      Score Test for Covariates with Fixed Effects in
                        Linear or Logistic Mixed Model
score.variance.linear   Variance Component Test in Linear or Logistic
                        Mixed Model
select.inds             Subsetting from a 'bed.matrix'
select.snps             Subsetting from a 'bed.matrix'
set.genomic.sex         Genomic Sex
set.hwe                 Hardy-Weinberg Equilibrium
set.stats               Basic statistics for a 'bed.matrix'
write.bed.matrix        Save a 'bed.matrix'
