Learn R Programming

⚠️There's a newer version (1.6) of this package.Take me there.

gap (version 0.4)

Genetic analysis package

Description

This is an integrated package for genetic data analysis of both population and family data. It currently includes sample size calculations for both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics for linkage and association analysis involving one or more genetic markers including haplotype analysis. The future plan includes incorporation of programs for path analysis, segregation, and other statistics in linkage and association analysis.

Copy Link

Version

Install

install.packages('gap')

Monthly Downloads

15,115

Version

0.4

License

Programs included in this package by Jing hua Zhao will be under GPL. Specific requirement may be possible for programs written by other authors.

Maintainer

Jing Zhao

Last Published

August 27th, 2024

Functions in gap (0.4)

gcontrol

genomic control
pbsize

Power for population-based association design
bt

Bradley-Terry model for contingency table
gc.em

Gene counting for haplotype analysis
hap.score

Score Statistics for Association of Traits with Haplotypes
aldh2

ALDH2 markers and Alcoholism
pfc

Probability of familial clustering of disease
mia

multiple imputation analysis for hap
whscore

Whittemore-Halpern scores for allele-sharing
tbyt

LD statistics for two SNPs
hwe.hardy

Hardy-Weinberg equlibrium test
s2k

Statistics for 2 by K table
makeped

A function to prepare pedigrees in post-MAKEPED format
kin.morgan

kinship matrix for simple pedigree
htr

Haplotype trend regression
fsnps

A case-control data involving four SNPs for missing genotype
kbyl

LD statistics for two multiallelic loci
muvar

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

Chow's test for heterogeneity in two regressions
hap

Haplotype reconstruction
gif

Kinship coefficient and genetic index of familiality
hap.em

Gene counting for haplotype analysis
genecounting

Gene counting for haplotype analysis
hla

HLA markers and Schizophrenia
fbsize

Sample size for family-based linkage and association design
apoeapoc

APOE/APOC1 markers and Schizophrenia
mtdt

Transmission/disequilibrium test of a multiallelic marker