R: Genetic analysis package

gap-package {gap} | R Documentation

## Genetic analysis package

### Description

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. Over years, the package has been developed in-between many projects hence also the name (gap).

### Details

Package: | gap
Version: | 1.2.3
Depends: | R(>= 2.1.0)
Suggests: | BradleyTerry2, MASS, Matrix, MCMCglmm, R2jags, bdsmatrix,
| calibrate, circlize, coda, cowplot, coxme, dplyr, foreign, forestplot,
| gap.datasets, ggplot2, grid, haplo.stats, kinship2, lattice,
| magic, matrixStats, meta, metafor, mets, nlme, pedigree, pedigreemm,
| plotrix, qqman, regress, reshape, rmeta, rms, survival
License: | GPL (>=2)
URL: | https://jinghuazhao.github.io/R

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
cs | Credibel set
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
gc.lambda | Estimation of the genomic control inflation statistic (lambda)
genecounting | Gene counting for haplotype analysis
gif | Kinship coefficient and genetic index of familiality
gsmr | Mendelian randomization analysis
hap | Haplotype reconstruction
hap.em | Gene counting for haplotype analysis
hap.score | Score statistics for association of traits with haplotypes
htr | Haplotype trend regression
h2.jags | Heritability estimation based on genomic relationship matrix using JAGS
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
hwe.jags | Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS
invnormal | inverse Normal transformation
kin.morgan | kinship matrix for simple pedigree
LD22 | LD statistics for two diallelic markers
LDkl | LD statistics for two multiallelic markers
lambda1000 | A standardized estimate of the genomic inflation scaling to
| a study of 1,000 cases and 1,000 controls
log10p | log10(p) for a standard normal deviate
logp | log(p) for a normal deviate
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
sentinels | Sentinel identification from GWAS summary statistics
tscc | Power calculation for two-stage case-control design
* GRAPHICS *
asplot | Regional association plot
ESplot | Effect-size plot
circos.cis.vs.trans.plot | circos plot of cis/trans classification
circos.cnvplot | circos plot of CNVs
circos.mhtplot | circos Manhattan plot with gene annotation
cnvplot | genomewide plot of CNVs
makeRLEplot | make relative log expression plot
METAL_forestplot | forest plot as R/meta's forest for METAL outputs
mhtplot | Manhattan plot
mhtplot2 | Manhattan plot with annotations
mhtplot2d | 2D Manhattan plot
mhtplot3d | 3D Manhattan plot
mhtplot.trunc | truncated Manhattan plot
miamiplot | Miami plot
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
* 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
chr_pos_a1_a2 | Form SNPID from chromosome, posistion and alleles
cis.vs.trans.classification | a cis/trans classifier
comp.score | score statistics for testing genetic linkage of quantitative trait
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
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
snptest_sample | A utility to generate SNPTEST sample file
whscore | Whittemore-Halpern scores for allele-sharing
weighted.median | Weighted median with interpolation

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.

### Author(s)

Author: Jing Hua Zhao in collaboration with other colleagues, and with help from Kurt Hornik and Brian Ripley of the R core development team

Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>

### References

Zhao JH, gap: genetic analysis package. Journal of Statistical Software 2007, 23(8):1-18

[Package gap version 1.2.3-1 Index]