| Package: |
| gap |
| Version: |
| 1.1-13 |
| Depends: |
| R(>= 2.1.0) |
| Suggests: |
| BradleyTerry2, MASS, Matrix, MCMCglmm, NCBI2R, bdsmatrix, coxme, foreign, grid, |
| haplo.stats, kinship2, magic, mets, nlme, pedigree, pedigreemm, regress, rms, survival |
| License: |
| GPL (>=2) |
| URL: |
| http://www.mrc-epid.cam.ac.uk/people/jing-hua-zhao |
Index:
| * ANALYSIS * |
| AE3 |
| AE model using nuclear family trios |
| bt |
| Bradley-Terry model for contingency table |
| ccsize |
| Power and sample size for case-cohort design |
| fbsize |
| Sample size for family-based linkage and association design |
| gc.em |
| Gene counting for haplotype analysis |
| gcontrol |
| genomic control |
| gcontrol2 |
| genomic control based on p values |
| gcp |
| Permutation tests using GENECOUNTING |
| genecounting |
| Gene counting for haplotype analysis |
| gif |
| Kinship coefficient and genetic index of familiality |
| hap |
| Haplotype reconstruction |
| hap.em |
| Gene counting for haplotype analysis |
| hap.score |
| Score statistics for association of traits with haplotypes |
| htr |
| Haplotype trend regression |
| hwe |
| Hardy-Weinberg equilibrium test for a multiallelic marker |
| hwe.cc |
| A likelihood ratio test of population Hardy-Weinberg equilibrium |
| hwe.hardy |
| Hardy-Weinberg equilibrium test using MCMC |
| kin.morgan |
| kinship matrix for simple pedigree |
| LD22 |
| LD statistics for two diallelic markers |
| LDkl |
| LD statistics for two multiallelic markers |
| masize |
| Sample size calculation for mediation analysis |
| MCMCgrm |
| Mixed modeling with genetic relationship matrices |
| mia |
| multiple imputation analysis for hap |
| mtdt |
| Transmission/disequilibrium test of a multiallelic marker |
| mtdt2 |
| Transmission/disequilibrium test of a multiallelic marker |
| by Bradley-Terry model |
| mvmeta |
| Multivariate meta-analysis based on generalized least squares |
| pbsize |
| Power for population-based association design |
| pbsize2 |
| Power for case-control association design |
| pfc |
| Probability of familial clustering of disease |
| pfc.sim |
| Probability of familial clustering of disease |
| pgc |
| Preparing weight for GENECOUNTING |
| print.hap.score |
| Print a hap.score object |
| s2k |
| Statistics for 2 by K table |
| tscc |
| Power calculation for two-stage case-control design |
* GRAPHICS * asplot Regional association plot ESplot Effect-size plot mhtplot Manhattan plot mhtplot2 Manhattan plot with annotations pedtodot Converting pedigree(s) to dot file(s) plot.hap.score Plot haplotype frequencies versus haplotype score statistics qqfun Quantile-comparison plots qqunif Q-Q plot for uniformly distributed random variable
* DATASETS * PD A study of Parkinson's disease and APOE, LRRK2, SNCA makers aldh2 ALDH2 markers and alcoholism apoeapoc APOE/APOC1 markers and schizophrenia cf Cystic Fibrosis data crohn Crohn's disease data fa Friedreich ataxia data fsnps A case-control data involving four SNPs with missing genotype hla HLA markers and schizophrenia l51 An example pedigree data lukas An example pedigree mao A study of Parkinson's disease and MAO gene meyer A pedigree data on 282 animals deriving from two generations nep499 A study of Alzheimer's disease with eight SNPs and APOE
* UTITLITIES * SNP Functions for single nucleotide polymorphisms (SNPs) BFDP Bayesian false-discovery probability FPRP False-positive report probability ab Test/Power calculation for mediating effect b2r Obtain correlation coefficients and their variance-covariances chow.test Chow's test for heterogeneity in two regressions comp.score score statistics for testing genetic linkage of quantitative trait h2 Heritability estimation according to twin correlations for case-control studies klem Haplotype frequency estimation based on a genotype table of two multiallelic markers makeped A function to prepare pedigrees in post-MAKEPED format metap Meta-analysis of p values metareg Fixed and random effects model for meta-analysis muvar Means and variances under 1- and 2- locus (diallelic) QTL model read.ms.output A utility function to read ms output twinan90 Classic twin models whscore Whittemore-Halpern scores for allele-sharing GRM functions ReadGRM, ReadGRMBin, ReadGRMPLINK, ReadGRMPCA, WriteGRM, WriteGRMBin, WriteGRMSAS handle genomic relationship matrix involving other software heritability functions h2G, VR, h2GC, h2l give point estimates as with their variances for continuous traits and binary traits under liability threshold model and case-control sampling
We have incorporated functions for a wide range of problems. Nevertheless, this largely remains as a preliminary work to be consolidated in the near future.