It is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.
| Package: | gap |
| Version: | 1.1-20 |
| 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.
Zhao JH, gap: genetic analysis package. Journal of Statistical Software 2007, 23(8):1-18