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gap (version 1.3-1)

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

install.packages('gap')

Monthly Downloads

14,766

Version

1.3-1

License

GPL (>= 2)

Issues

4

Pull Requests

0

Stars

12

Forks

4

Maintainer

Jing Zhao

Last Published

October 21st, 2022

Functions in gap (1.3-1)

LDkl

LD statistics for two multiallelic markers
MCMCgrm

Mixed modeling with genetic relationship matrices
snp.ES

Functions for single nucleotide polymorphisms (SNPs)
circos.cnvplot

circos plot of CNVs.
circos.mhtplot

circos Manhattan plot with gene annotation
METAL_forestplot

forest plot as R/meta's forest for METAL outputs
circos.cis.vs.trans.plot

circos plot of cis/trans classification
circos.mhtplot2

Another circos Manhattan plot
gcontrol

genomic control
cnvplot

genomewide plot of CNVs
cis.vs.trans.classification

A cis/trans classifier
chr_pos_a1_a2

SNP id by chr:pos+a1/a2
ccsize

Power and sample size for case-cohort design
gc.lambda

Estionmation of the genomic control inflation statistic (lambda)
chow.test

Chow's test for heterogeneity in two regressions
gc.em

Gene counting for haplotype analysis
gap-package

Genetic analysis package
comp.score

score statistics for testing genetic linkage of quantitative trait
grid2d

Two-dimensional grid
gcontrol2

genomic control based on p values
gif

Kinship coefficient and genetic index of familiality
gsmr

Mendelian randomization analysis
h2.jags

Heritability estimation based on genomic relationship matrix using JAGS
genecounting

Gene counting for haplotype analysis
bt

Bradley-Terry model for contingency table
cs

Credible set
gcp

Permutation tests using GENECOUNTING
get_pve_se

Get pve and its standard error from n, z
fbsize

Sample size for family-based linkage and association design
gap-internal

Internal functions for gap
get_b_se

Get b and se from AF, n, and z
b2r

Obtain correlation coefficients and their variance-covariances
asplot

Regional association plot
get_sdy

Get sd(y) from AF, n, b, se
h2l

Heritability under the liability threshold model
hap

Haplotype reconstruction
hwe

Hardy-Weinberg equlibrium test for a multiallelic marker
hmht.control

Controls for highlights
htr

Haplotype trend regression
hap.score

Score statistics for association of traits with haplotypes
h2G

Heritability and its variance
hwe.hardy

Hardy-Weinberg equilibrium test using MCMC
h2GE

Heritability and its variance when there is an environment component
h2_mzdz

Heritability estimation according to twin correlations
hwe.jags

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS
hwe.cc

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

kinship matrix for simple pedigree
klem

Haplotype frequency estimation based on a genotype table of two multiallelic markers
log10p

log10(p) for a normal deviate z
labelManhattan

Annotate Manhattan or Miami Plot
hap.em

Gene counting for haplotype analysis
makeped

A function to prepare pedigrees in post-MAKEPED format
log10pvalue

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

Truncated Manhattan plot
invnormal

Inverse normal transformation
mht.control

Controls for mhtplot
ixy

Conversion of chrosome name from strings
logp

log(p) for a normal deviate z
inv_chr_pos_a1_a2

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

Meta-analysis of p values
mhtplot

Manhattan plot
mhtplot2

Manhattan plot with annotations
metareg

Fixed and random effects model for meta-analysis
masize

Sample size calculation for mediation analysis
miamiplot

Miami plot
pbsize2

Power for case-control association design
mia

Multiple imputation analysis for hap
pbsize

Power for population-based association design
mvmeta

Multivariate meta-analysis based on generalized least squares
miamiplot2

Miami Plot
muvar

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

Transmission/disequilibrium test of a multiallelic marker
mtdt2

Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model
print.hap.score

Print a hap.score object
pvalue

P value for a normal deviate
pfc.sim

Probability of familial clustering of disease
pfc

Probability of familial clustering of disease
qqunif

Q-Q plot for uniformly distributed random variable
qtl2dplotly

2D QTL plotly
mr_forestplot

Mendelian Randomization forest plot
qtl2dplot

2D QTL plot
pgc

Preparing weight for GENECOUNTING
plot.hap.score

Plot haplotype frequencies versus haplotype score statistics
qtlClassifier

A QTL cis/trans classifier
qtl3dplotly

3D QTL plot
xy

Conversion of chromosome names to strings
qqfun

Quantile-comparison plots
runshinygap

Start shinygap
pedtodot_verbatim

Pedigree-drawing with graphviz
read.ms.output

A utility function to read ms output
s2k

Statistics for 2 by K table
tscc

Power calculation for two-stage case-control design
whscore

Whittemore-Halpern scores for allele-sharing
pedtodot

Converting pedigree(s) to dot file(s)
revStrand

Allele on the reverse strand
sentinels

Sentinel identification from GWAS summary statistics
snptest_sample

A utility to generate SNPTEST sample file
LD22

LD statistics for two diallelic markers
BFDP

Bayesian false-discovery probability
AE3

AE model using nuclear family trios
ab

Test/Power calculation for mediating effect
ESplot

Effect-size plot
FPRP

False-positive report probability