Genetic risk scores for serum lipid levels
Parameter format for multi-SNP analyses
Calculate approximate Bayes factor (ABF) for normal prior.
Genetic risk score for height.
Genetic risk scores for glucose/insulin traits.
Class for SNP genotype and phenotype data.
Multi-phenotype test for association
Filter SNPs for inclusion in genetic risk score using
heterogeneity test.
Fit normal linear model using pre-built matrix of second moments.
Simulate from finite mixture of univariate Gaussian densities.
Builds a matrix of second moments for a set of individuals, from the
matrices of second moments for all constituent subsets of individuals.
For finite mixture of univariate Gaussian densities, computes
proportion of variance explained by the mixture labels.
Plot empirical density and components and total density for finite mixture of univariate Gaussian densities.
Extract individual level snp/haplotype data from HapMap
Calculate weights and transformed phenotype so that one iteration
of generalised least squares approximates a logistic regression.
Class for summary statistic matrix of second moments.
Genetics ToolboX
Simulated example finemapping genotype and phenotype data.
Stepwise downward model selection using summary statistic matrix.
Convenience tool to fit a series of single-SNP models.
Exact test of Hardy--Weinberg.
Update genotype coding when there are coded allele designation flips.
Coefficient extractor for fitted models.
Read genotype dosages in the format output by MACH
Remap coordinates from BLAT query sequence to BLAT target sequence.
Match with multiple matching possible.
Genetic risk score calculation from summary statistics.
Read hapmap haplotypes.
Build matrix of second moments from subject-specific data.
Parse text representation of a SNP embedded in flanking sequences.
Hypertension association statistics for SNPs near the AGT gene.
Estimate regression coefficients using quadratic approximation to likelihood function.
Make genetic risk scores from individual-level data.
Genetic risk scores for blood pressure.
Genotyping array annotation for SNPs near the BRCA1 gene.
Calculate approximate Bayes factor (ABF) using method of
Wakefield (2009).
Fit finite mixture of univariate Gaussian densities to data.
Test approximation used in genetic risk score analyses.
Read genotype dosages in the format output by PLINK.
Calculate approximate Bayes factor (ABF) for t distribution prior.
Genetic risk scores for coronary artery disease risk
Simulated example genotype and longitudinal phenotype data.
Paste together (vectors of) A and B alleles after sorting alphabetically.
Diagnostic plot for genetic risk score calculation from summary statistics.
Stepwise upward model selection using summary statistic matrix.
Genetic risk scores for type 2 diabetes risk.
Read genotype dosages in the format output by IMPUTE.
Read genotype dosages in the format output by minimac
Remove leading and trailing spaces; convert double spaces to
single spaces.
Exact test of Hardy--Weinberg.