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gap (version 1.6)

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

10,481

Version

1.6

License

GPL (>= 2)

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Repository

https://github.com/jinghuazhao/R

Maintainer

Last Published

August 27th, 2024

Functions in gap (1.6)

Allele recoding

Regional association plot

cis.vs.trans.classification

A cis/trans classifier

A function to read GRM binary files

genomewide plot of CNVs

circos plot of CNVs.

circos.cis.vs.trans.plot

circos plot of cis/trans classification

Power and sample size for case-cohort design

Chow's test for heterogeneity in two regressions

score statistics for testing genetic linkage of quantitative trait

genomic control

Estimation of the genomic control inflation statistic (lambda)

Gene counting for haplotype analysis

Heritability estimation based on genomic relationship matrix using JAGS

Two-dimensional grid

Get b and se from AF, n, and z

Get pve and its standard error from n, z

Genetic analysis package

circos.mhtplot2

Another circos Manhattan plot

circos Manhattan plot with gene annotation

genomic control based on p values

Functions for single nucleotide polymorphisms

Gene counting for haplotype analysis

Gene counting for haplotype analysis

Score statistics for association of traits with haplotypes

Heritability and its variance

Effect size and standard error from confidence interval

SNP id by chr:pos+a1/a2

Heritability and its variance when there is an environment component

Permutation tests using GENECOUNTING

Heritability under the liability threshold model

Heritability estimation according to twin correlations

Chromosomal lengths for build 37

Genotype recoding

Chromosomal lengths for build 36

Hardy-Weinberg equilibrium test using MCMC

kinship matrix for simple pedigree

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

Inverse normal transformation

Conversion of chrosome name from strings

A function to prepare pedigrees in post-MAKEPED format

Sample size for family-based linkage and association design

Fixed and random effects model for meta-analysis

Meta-analysis of p values

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

Sample size calculation for mediation analysis

Haplotype reconstruction

Control for haplotype reconstruction

Manhattan plot with annotations

Truncated Manhattan plot

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

log(p) for a normal deviate z

Multiple imputation analysis for hap

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

Controls for mhtplot

inv_chr_pos_a1_a2

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

Power for case-control association design

pedtodot_verbatim

Pedigree-drawing with graphviz

Probability of familial clustering of disease

Converting pedigree(s) to dot file(s)

Preparing weight for GENECOUNTING

Conversion of a genotype identifier to alleles

Mendelian randomization analysis

Probability of familial clustering of disease

Q-Q plot for uniformly distributed random variable

Chromosomal lengths for build 38

Kinship coefficient and genetic index of familiality

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

Controls for highlights

log10(p) for a normal deviate z

Hardy-Weinberg equlibrium test for a multiallelic marker

Annotate Manhattan or Miami Plot

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

Plot haplotype frequencies versus haplotype score statistics

Whittemore-Halpern scores for allele-sharing

Power calculation for two-stage case-control design

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

Haplotype trend regression

Multivariate meta-analysis based on generalized least squares

A QTL cis/trans classifier

Allele on the reverse strand

A utility function to read ms output

Power for population-based association design

print.hap.score

Print a hap.score object

A utility to generate SNPTEST sample file

Distance-based signal identification

Mendelian Randomization forest plot

Sentinel identification from GWAS summary statistics

Statistics for 2 by K table

P value for a normal deviate

Transmission/disequilibrium test of a multiallelic marker

Conversion of chromosome names to strings

Quantile-comparison plots

LD statistics for two multiallelic markers

A function to read GRM file

Disease prevalences in cases and controls

A function to write GRM binary file

METAL_forestplot

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

A function to write GRM file

LD statistics for two diallelic markers

Mixed modeling with genetic relationship matrices

Obtain correlation coefficients and their variance-covariances

Effect-size plot

False-positive report probability

Bayesian false-discovery probability

Allele-to-genotype conversion

Bradley-Terry model for contingency table

Test/Power calculation for mediating effect

AE model using nuclear family trios