Man pages for gaston
Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
| AGT | AGT data set |
| as.bed.matrix | Creation of a bed.matrix |
| association.test | Association Test |
| bed.loadings | SNP loadings |
| bed.matrix-class | Class '"bed.matrix"' |
| DM | Dominance Matrix |
| dupli | Small data set to illustrate 'SNP.rm.duplicates' |
| gaston-package | gaston |
| GRM | Genetic Relationship Matrix |
| is.autosome | Autosomes and X, Y, MT chromosomes |
| LCT | LCT data set |
| LD | Linkage Disequilibrium |
| LD.clump | LD clumping |
| 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.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... |
| 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 | Score Test for Covariates with Fixed Effects in Linear or... |
| score.variance | 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' |
| SNP.duplicated | Duplicated SNPs |
| SNP.match | SNP matching |
| SNP.rm.duplicates | Remove duplicated SNPs |
| Tests | Evaluation of a condition on SNPS or individuals in a... |
| TTN | TTN data set |
| write.bed.matrix | Save a 'bed.matrix' |
