AGT                     AGT data set
DM                      Dominance Matrix
GRM                     Genetic Relationship Matrix
LCT                     LCT data set
LD                      Linkage Disequilibrium
LD.clump                LD clumping
LD.plot                 Plot Linkage Disequilibrium
LD.thin                 LD thinning
SNP.duplicated          Duplicated SNPs
SNP.match               SNP matching
SNP.rm.duplicates       Remove duplicated SNPs
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"'
dupli                   Small data set to illustrate
                        'SNP.rm.duplicates'
gaston-package          gaston
is.autosome             Autosomes and X, Y, MT chromosomes
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.restricted.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
manhattan               Manhattan plot
qqplot.pvalues          QQ plot of p-values
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.dist                Set Genetic Distance
set.genomic.sex         Genomic Sex
set.hwe                 Hardy-Weinberg Equilibrium
set.stats               Basic statistics for a 'bed.matrix'
test.inds               Evaluation of a condition on SNPS or
                        individuals in a 'bed.matrix'
write.bed.matrix        Save a 'bed.matrix'
