| gaston-package | gaston | 
| %*%-method | Class '"bed.matrix"' | 
| AGT | AGT data set | 
| AGT.bim | AGT data set | 
| AGT.fam | AGT data set | 
| AGT.gen | AGT data set | 
| AGT.pop | AGT data set | 
| as.bed.matrix | Creation of a bed.matrix | 
| as.matrix-method | Class '"bed.matrix"' | 
| association.test | Association Test | 
| bed.loadings | SNP loadings | 
| bed.matrix | Class '"bed.matrix"' | 
| bed.matrix-class | Class '"bed.matrix"' | 
| cbind | Class '"bed.matrix"' | 
| cbind-method | Class '"bed.matrix"' | 
| coerce-method | Class '"bed.matrix"' | 
| dim-method | Class '"bed.matrix"' | 
| DM | Dominance Matrix | 
| dupli | Small data set to illustrate 'SNP.rm.duplicates' | 
| dupli.bim | Small data set to illustrate 'SNP.rm.duplicates' | 
| dupli.gen | Small data set to illustrate 'SNP.rm.duplicates' | 
| dupli.ped | Small data set to illustrate 'SNP.rm.duplicates' | 
| dupli.pop | Small data set to illustrate 'SNP.rm.duplicates' | 
| gaston | gaston | 
| GRM | Genetic Relationship Matrix | 
| head-method | Class '"bed.matrix"' | 
| is.autosome | Autosomes and X, Y, MT chromosomes | 
| is.chr.mt | Autosomes and X, Y, MT chromosomes | 
| is.chr.x | Autosomes and X, Y, MT chromosomes | 
| is.chr.y | Autosomes and X, Y, MT chromosomes | 
| LCT | LCT data set | 
| LCT.bim | LCT data set | 
| LCT.fam | LCT data set | 
| LCT.gen | LCT data set | 
| LCT.pop | LCT data set | 
| LD | Linkage Disequilibrium | 
| LD.plot | Plot Linkage Disequilibrium | 
| LD.thin | LD thinning | 
| 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.diago.profile.likelihood | Likelihood of a linear mixed model | 
| lmm.profile.restricted.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 | 
| matrix-method | Class '"bed.matrix"' | 
| mu | Class '"bed.matrix"' | 
| mu-method | Class '"bed.matrix"' | 
| mu<- | Class '"bed.matrix"' | 
| mu<--method | Class '"bed.matrix"' | 
| p | Class '"bed.matrix"' | 
| p-method | Class '"bed.matrix"' | 
| p<- | Class '"bed.matrix"' | 
| p<--method | Class '"bed.matrix"' | 
| qqplot.pvalues | QQ plot of p-values | 
| random.pm | Random square definite positive matrix | 
| rbind | Class '"bed.matrix"' | 
| rbind-method | Class '"bed.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.fixed.logistic | 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 | 
| score.variance.logistic | 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' | 
| set.stats.ped | Basic statistics for a 'bed.matrix' | 
| set.stats.snps | Basic statistics for a 'bed.matrix' | 
| show-method | Class '"bed.matrix"' | 
| sigma | Class '"bed.matrix"' | 
| sigma-method | Class '"bed.matrix"' | 
| sigma<- | Class '"bed.matrix"' | 
| sigma<--method | Class '"bed.matrix"' | 
| SNP.duplicated | Duplicated SNPs | 
| SNP.match | SNP matching | 
| SNP.rm.duplicates | Remove duplicated SNPs | 
| standardize | Class '"bed.matrix"' | 
| standardize-method | Class '"bed.matrix"' | 
| standardize<- | Class '"bed.matrix"' | 
| standardize<--method | Class '"bed.matrix"' | 
| test.inds | Evaluation of a condition on SNPS or individuals in a 'bed.matrix' | 
| test.snps | Evaluation of a condition on SNPS or individuals in a 'bed.matrix' | 
| TTN | TTN data set | 
| TTN.bim | TTN data set | 
| TTN.fam | TTN data set | 
| TTN.gen | TTN data set | 
| TTN.pop | TTN data set | 
| which.inds | Evaluation of a condition on SNPS or individuals in a 'bed.matrix' | 
| which.snps | Evaluation of a condition on SNPS or individuals in a 'bed.matrix' | 
| write.bed.matrix | Save a 'bed.matrix' | 
| [-method | Class '"bed.matrix"' |