Genetics ToolboX


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Documentation for package ‘gtx’ version 0.0.8

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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.