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