Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Creation of a bed.matrix
Association Test
SNP loadings
Class "bed.matrix"
Dominance Matrix
gaston
Genetic Relationship Matrix
Autosomes and X, Y, MT chromosomes
LD clumping
Plot Linkage Disequilibrium
Linkage Disequilibrium
LD thinning
Contour plot for two parameters likelihood
Linear mixed model fitting with AIREML
Likelihood of a linear mixed model
Linear mixed model fitting with the diagonalization trick
Likelihood of a linear mixed model
Linear mixed model data simulation
Logistic mixed model fitting with Penalized Quasi-Likelihood / AIREML
Manhattan plot
QQ plot of p-values
Random square definite positive matrix
Read a bed.matrix
Create a bed.matrix from VCF files
Reshape a Genetic Relationship Matrix
Score Test for Covariates with Fixed Effects in Linear or Logistic Mix...
Variance Component Test in Linear or Logistic Mixed Model
Subsetting from a bed.matrix
Subsetting from a bed.matrix
Set Genetic Distance
Genomic Sex
Hardy-Weinberg Equilibrium
Basic statistics for a bed.matrix
Duplicated SNPs
SNP matching
Remove duplicated SNPs
Evaluation of a condition on SNPS or individuals in a bed.matrix
Save a bed.matrix
Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.