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| 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 |
| 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. |
| est.moments2 | Estimate regression coefficients using quadratic approximation to likelihood function. |
| 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.snpdata | Class for SNP genotype and phenotype data. |
| lipid.scores | Genetic risk scores for serum lipid levels |
| 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. |
| mthfr.params | Simulated example finemapping genotype and phenotype data. |
| mthfrex | Simulated example finemapping genotype and phenotype data. |
| 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.plink | Read genotype dosages in the format output by PLINK. |
| snpdata | Class for SNP genotype and phenotype data. |
| 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. |