Genetics ToolboX

abf.normal | Calculate approximate Bayes factor (ABF) for normal prior. |

abf.t | Calculate approximate Bayes factor (ABF) for t distribution... |

abf.Wakefield | Calculate approximate Bayes factor (ABF) using method of... |

agtstats | Hypertension association statistics for SNPs near the AGT... |

align.snpdata.coding | Update genotype coding when there are coded allele... |

allelesAB | Paste together (vectors of) A and B alleles after sorting... |

bp.scores | Genetic risk scores for blood pressure. |

cad.scores | Genetic risk scores for coronary artery disease risk |

coeff.extract | Coefficient extractor for fitted models. |

combine.moments2 | Builds a matrix of second moments for a set of individuals,... |

contrasting.rainbow | Rainbow of colours permuted to maximise contrast. |

est.moments2 | Estimate regression coefficients using quadratic... |

fitmix | Fit finite mixture of univariate Gaussian densities to data. |

fitmix.plot | Plot empirical density and components and total density for... |

fitmix.r2 | For finite mixture of univariate Gaussian densities, computes... |

fitmix.simulate | Simulate from finite mixture of univariate Gaussian... |

gls.approx.logistic | Calculate weights and transformed phenotype so that one... |

grs.filter.Qrs | Filter SNPs for inclusion in genetic risk score using... |

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... |

grs.summary | Genetic risk score calculation from summary statistics. |

gtx-package | 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. |

lipid.cad.scores | Genetic risk scores for serum lipid levels and coronary... |

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... |

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. |

mthfrex | Simulated example finemapping genotype and phenotype data. |

multimatch | Match with multiple matching possible. |

multipheno.T2 | Multi-phenotype test for association |

ncp | Compute non-centrality parameter of chi squared distribution. |

parse.snps | Parse text representation of a SNP embedded in flanking... |

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... |

sanitise.whitespace | Remove leading and trailing spaces; convert double spaces to... |

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... |

stepup.moments2 | Stepwise upward model selection using summary statistic... |

t2dex | Simulated example genotype and longitudinal phenotype data. |

t2d.scores | Genetic risk scores for type 2 diabetes risk. |

test.subsample | Test approximation used in genetic risk score analyses. |

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