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