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gap (version 1.5)

Genetic Analysis Package

Description

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. ], 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, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

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Install

install.packages('gap')

Monthly Downloads

15,115

Version

1.5

License

GPL (>= 2)

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Repository

https://github.com/jinghuazhao/R

Maintainer

Jing Zhao

Last Published

January 13th, 2023

Functions in gap (1.5)

Disease prevalences in cases and controls

Mixed modeling with genetic relationship matrices

Functions for single nucleotide polymorphisms (SNPs)

False-positive report probability

Bayesian false-discovery probability

LD statistics for two diallelic markers

LD statistics for two multiallelic markers

circos Manhattan plot with gene annotation

circos plot of CNVs.

Power and sample size for case-cohort design

SNP id by chr:pos+a1/a2

METAL_forestplot

forest plot as R/meta's forest for METAL outputs

circos.cis.vs.trans.plot

circos plot of cis/trans classification

Regional association plot

Chow's test for heterogeneity in two regressions

Bradley-Terry model for contingency table

Test/Power calculation for mediating effect

Obtain correlation coefficients and their variance-covariances

circos.mhtplot2

Another circos Manhattan plot

genomewide plot of CNVs

score statistics for testing genetic linkage of quantitative trait

cis.vs.trans.classification

A cis/trans classifier

Gene counting for haplotype analysis

Estionmation of the genomic control inflation statistic (lambda)

Kinship coefficient and genetic index of familiality

Get pve and its standard error from n, z

Get b and se from AF, n, and z

Get sd(y) from AF, n, b, se

genomic control based on p values

genomic control

Sample size for family-based linkage and association design

Permutation tests using GENECOUNTING

Heritability estimation based on genomic relationship matrix using JAGS

Two-dimensional grid

Gene counting for haplotype analysis

Internal functions for gap

Genetic analysis package

Score statistics for association of traits with haplotypes

Heritability and its variance when there is an environment component

Heritability and its variance

Gene counting for haplotype analysis

Haplotype frequency estimation based on a genotype table of two multiallelic markers

Heritability under the liability threshold model

Controls for highlights

Heritability estimation according to twin correlations

Hardy-Weinberg equlibrium test for a multiallelic marker

Inverse normal transformation

inv_chr_pos_a1_a2

Retrieval of chr:pos+a1/a2 according to SNP id

Conversion of chrosome name from strings

Control for haplotype reconstruction

Hardy-Weinberg equilibrium test using MCMC

kinship matrix for simple pedigree

Haplotype trend regression

Haplotype reconstruction

A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

log10(p) for a normal deviate z

Annotate Manhattan or Miami Plot

log10(p) for a P value including its scientific format

Sample size calculation for mediation analysis

Meta-analysis of p values

Controls for mhtplot

log(p) for a normal deviate z

Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model

Multiple imputation analysis for hap

A function to prepare pedigrees in post-MAKEPED format

Transmission/disequilibrium test of a multiallelic marker

Truncated Manhattan plot

Fixed and random effects model for meta-analysis

Multivariate meta-analysis based on generalized least squares

Manhattan plot with annotations

Means and variances under 1- and 2- locus (biallelic) QTL model

Mendelian Randomization forest plot

Mendelian randomization analysis

Converting pedigree(s) to dot file(s)

Probability of familial clustering of disease

Probability of familial clustering of disease

pedtodot_verbatim

Pedigree-drawing with graphviz

P value for a normal deviate

Statistics for 2 by K table

print.hap.score

Print a hap.score object

Allele on the reverse strand

Plot haplotype frequencies versus haplotype score statistics

Preparing weight for GENECOUNTING

A utility function to read ms output

Conversion of chromosome names to strings

Q-Q plot for uniformly distributed random variable

Quantile-comparison plots

A utility to generate SNPTEST sample file

Sentinel identification from GWAS summary statistics

Power for population-based association design

Power for case-control association design

Whittemore-Halpern scores for allele-sharing

A QTL cis/trans classifier

Power calculation for two-stage case-control design

AE model using nuclear family trios

Effect-size plot