gtx-package |
Genetics ToolboX |
abf.normal |
Calculate approximate Bayes factor (ABF) for normal prior. |
abf.t |
Calculate approximate Bayes factor (ABF) for t distribution prior. |
abf.Wakefield |
Calculate approximate Bayes factor (ABF) using method of Wakefield (2009). |
agtstats |
Hypertension association statistics for SNPs near the AGT gene. |
align.snpdata.coding |
Update genotype coding when there are coded allele designation flips. |
allelesAB |
Paste together (vectors of) A and B alleles after sorting alphabetically. |
as.snpdata |
Class for SNP genotype and phenotype data. |
bp.scores |
Genetic risk scores for blood pressure. |
cad.scores |
Genetic risk scores for coronary artery disease risk |
chi2ncp |
Compute non-centrality parameter of chi squared distribution. |
coeff.extract |
Coefficient extractor for fitted models. |
combine.moments2 |
Builds a matrix of second moments for a set of individuals, from the matrices of second moments for all constituent subsets of individuals. |
contrasting.rainbow |
Rainbow of colours permuted to maximise contrast. |
est.moments2 |
Estimate regression coefficients using quadratic approximation to likelihood function. |
fitmix |
Fit finite mixture of univariate Gaussian densities to data. |
fitmix.plot |
Plot empirical density and components and total density for finite mixture of univariate Gaussian densities. |
fitmix.r2 |
For finite mixture of univariate Gaussian densities, computes proportion of variance explained by the mixture labels. |
fitmix.simulate |
Simulate from finite mixture of univariate Gaussian densities. |
gls.approx.logistic |
Calculate weights and transformed phenotype so that one iteration of generalised least squares approximates a logistic regression. |
grs.filter.Qrs |
Filter SNPs for inclusion in genetic risk score using heterogeneity test. |
grs.make.scores |
Make genetic risk scores from individual-level data. |
grs.onesnp.apply |
Convenience tool to fit a series of single-SNP models. |
grs.plot |
Diagnostic plot for genetic risk score calculation from summary statistics. |
grs.summary |
Genetic risk score calculation from summary statistics. |
gtx |
Genetics ToolboX |
gtx.params |
Parameter format for multi-SNP analyses |
hapmap.read.haplotypes |
Read hapmap haplotypes. |
hapmap.snpdata |
Extract individual level snp/haplotype data from HapMap |
height.scores |
Genetic risk score for height. |
is.moments2 |
Class for summary statistic matrix of second moments. |
is.snpdata |
Class for SNP genotype and phenotype data. |
lipid.cad.scores |
Genetic risk scores for serum lipid levels and coronary artery disease outcome |
lipid.scores |
Genetic risk scores for serum lipid levels |
liver.scores |
Genetic risk scores for liver enzyme traits. |
lm.moments2 |
Fit normal linear model using pre-built matrix of second moments. |
magic.scores |
Genetic risk scores for glucose/insulin traits. |
make.moments2 |
Build matrix of second moments from subject-specific data. |
mincover |
Compute minimum size of cover of overlapping intervals. |
moments2 |
Class for summary statistic matrix of second moments. |
mthfr.params |
Simulated example finemapping genotype and phenotype data. |
mthfrex |
Simulated example finemapping genotype and phenotype data. |
multimatch |
Match with multiple matching possible. |
multipheno.T2 |
Multi-phenotype test for association |
parse.snps |
Parse text representation of a SNP embedded in flanking sequences. |
read.snpdata.impute |
Read genotype dosages in the format output by IMPUTE. |
read.snpdata.mach |
Read genotype dosages in the format output by MACH |
read.snpdata.minimac |
Read genotype dosages in the format output by minimac |
read.snpdata.plink |
Read genotype dosages in the format output by PLINK. |
remap.q2t |
Remap coordinates from BLAT query sequence to BLAT target sequence. |
sanitise.whitespace |
Remove leading and trailing spaces; convert double spaces to single spaces. |
snpdata |
Class for SNP genotype and phenotype data. |
snphwe |
Exact test of Hardy-Weinberg. |
snphweCounts |
Exact test of Hardy-Weinberg. |
snps.BRCA1 |
Genotyping array annotation for SNPs near the BRCA1 gene. |
stepdown.moments2 |
Stepwise downward model selection using summary statistic matrix. |
stepup.moments2 |
Stepwise upward model selection using summary statistic matrix. |
summary.snpdata |
Class for SNP genotype and phenotype data. |
t2d.scores |
Genetic risk scores for type 2 diabetes risk. |
t2dex |
Simulated example genotype and longitudinal phenotype data. |