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gap (version 1.5-1)

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.packages('gap')

Monthly Downloads

13,389

Version

1.5-1

License

GPL (>= 2)

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Repository

https://github.com/jinghuazhao/R

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Last Published

January 22nd, 2023

Functions in gap (1.5-1)

LD statistics for two multiallelic markers

Disease prevalences in cases and controls

A function to read GRM file

METAL_forestplot

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

Bayesian false-discovery probability

LD statistics for two diallelic markers

False-positive report probability

AE model using nuclear family trios

Mixed modeling with genetic relationship matrices

Effect-size plot

Allele-to-genotype conversion

A function to write GRM file

A function to write GRM binary file

Regional association plot

Allele recoding

Test/Power calculation for mediating effect

A function to read GRM binary files

Functions for single nucleotide polymorphisms (SNPs)

Obtain correlation coefficients and their variance-covariances

Bradley-Terry model for contingency table

Power and sample size for case-cohort design

circos.cis.vs.trans.plot

circos plot of cis/trans classification

SNP id by chr:pos+a1/a2

circos.mhtplot2

Another circos Manhattan plot

cis.vs.trans.classification

A cis/trans classifier

Chow's test for heterogeneity in two regressions

genomewide plot of CNVs

score statistics for testing genetic linkage of quantitative trait

circos plot of CNVs.

circos Manhattan plot with gene annotation

Estionmation of the genomic control inflation statistic (lambda)

Gene counting for haplotype analysis

Conversion of a genotype identifier to alleles

Genetic analysis package

Internal functions for gap

genomic control

genomic control based on p values

Sample size for family-based linkage and association design

Permutation tests using GENECOUNTING

Get b and se from AF, n, and z

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

Get pve and its standard error from n, z

Heritability and its variance

Gene counting for haplotype analysis

Genotype recoding

Control for haplotype reconstruction

Haplotype reconstruction

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

Annotate Manhattan or Miami Plot

Kinship coefficient and genetic index of familiality

Heritability and its variance when there is an environment component

Controls for highlights

Hardy-Weinberg equilibrium test using MCMC

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

Hardy-Weinberg equlibrium test for a multiallelic marker

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

Haplotype trend regression

Two-dimensional grid

Truncated Manhattan plot

Heritability estimation based on genomic relationship matrix using JAGS

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

log10(p) for a normal deviate z

Meta-analysis of p values

Sample size calculation for mediation analysis

Mendelian randomization analysis

Mendelian Randomization forest plot

Multivariate meta-analysis based on generalized least squares

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

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

Transmission/disequilibrium test of a multiallelic marker

Fixed and random effects model for meta-analysis

Controls for mhtplot

pedtodot_verbatim

Pedigree-drawing with graphviz

Converting pedigree(s) to dot file(s)

Gene counting for haplotype analysis

Sentinel identification from GWAS summary statistics

Heritability estimation according to twin correlations

Preparing weight for GENECOUNTING

Plot haplotype frequencies versus haplotype score statistics

A QTL cis/trans classifier

Quantile-comparison plots

Q-Q plot for uniformly distributed random variable

Statistics for 2 by K table

Heritability under the liability threshold model

A utility to generate SNPTEST sample file

Score statistics for association of traits with haplotypes

Conversion of chrosome name from strings

Manhattan plot with annotations

Multiple imputation analysis for hap

kinship matrix for simple pedigree

inv_chr_pos_a1_a2

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

Inverse normal transformation

Power for population-based association design

print.hap.score

Print a hap.score object

Power for case-control association design

log(p) for a normal deviate z

A function to prepare pedigrees in post-MAKEPED format

Probability of familial clustering of disease

Probability of familial clustering of disease

Allele on the reverse strand

A utility function to read ms output

P value for a normal deviate

Conversion of chromosome names to strings

Power calculation for two-stage case-control design

Whittemore-Halpern scores for allele-sharing