gap: Genetic Analysis Package

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.

AuthorJing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley
Date of publication2015-06-06 08:56:06
MaintainerJing Hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>
LicenseGPL (>= 2)
Version1.1-16
http://www.mrc-epid.cam.ac.uk/people/jing-hua-zhao/

View on CRAN

Man pages

ab: Test/Power calculation for mediating effect

AE3: AE model using nuclear family trios

aldh2: ALDH2 markers and Alcoholism

apoeapoc: APOE/APOC1 markers and Alzheimer's

asplot: Regional association plot

b2r: Obtain correlation coefficients and their...

BFDP: Bayesian false-discovery probability

bt: Bradley-Terry model for contingency table

ccsize: Power and sample size for case-cohort design

CDKN: Example data for association plot

cf: Cystic fibrosis data

chow.test: Chow's test for heterogeneity in two regressions

comp.score: score statistics for testing genetic linkage of quantitative...

crohn: Crohn's disease data

ESplot: Effect-size plot

fa: Friedreich Ataxia data

fbsize: Sample size for family-based linkage and association design

FPRP: False-positive report probability

fsnps: A case-control data involving four SNPs with missing genotype

gap-internal: Internal functions for gap

gap-package: Genetic analysis package

gc.em: Gene counting for haplotype analysis

gcontrol: genomic control

gcontrol2: genomic control based on p values

gcp: Permutation tests using GENECOUNTING

genecounting: Gene counting for haplotype analysis

gif: Kinship coefficient and genetic index of familiality

h2: Heritability estimation according to twin correlations

hap: Haplotype reconstruction

hap.em: Gene counting for haplotype analysis

hap.score: Score statistics for association of traits with haplotypes

hla: The HLA data

hr1420: An example data for Manhattan plot with annotation

htr: Haplotype trend regression

hwe: Hardy-Weinberg equlibrium test for a multiallelic marker

hwe.cc: A likelihood ratio test of population Hardy-Weinberg...

hwe.hardy: Hardy-Weinberg equilibrium test using MCMC

kin.morgan: kinship matrix for simple pedigree

klem: Haplotype frequency estimation based on a genotype table of...

l51: An example pedigree data

LD22: LD statistics for two diallelic markers

LDkl: LD statistics for two multiallelic markers

lukas: An example pedigree

makeped: A function to prepare pedigrees in post-MAKEPED format

mao: A study of Parkinson's disease and MAO gene

masize: Sample size calculation for mediation analysis

MCMCgrm: Mixed modeling with genetic relationship matrices

metap: Meta-analysis of p values

metareg: Fixed and random effects model for meta-analysis

meyer: A pedigree data on 282 animals deriving from two generations

mfblong: Example data for ACEnucfam

mhtdata: An example data for Manhattan plot

mhtplot: Manhattan plot

mhtplot2: Manhattan plot with annotations

mia: multiple imputation analysis for hap

mtdt: Transmission/disequilibrium test of a multiallelic marker

mtdt2: Transmission/disequilibrium test of a multiallelic marker by...

muvar: Means and variances under 1- and 2- locus (biallelic) QTL...

mvmeta: Multivariate meta-analysis based on generalized least squares

nep499: A study of Alzheimer's disease with eight SNPs and APOE

pbsize: Power for population-based association design

pbsize2: Power for case-control association design

PD: A study of Parkinson's disease and APOE, LRRK2, SNCA makers

pedtodot: Converting pedigree(s) to dot file(s)

pfc: Probability of familial clustering of disease

pfc.sim: Probability of familial clustering of disease

pgc: Preparing weight for GENECOUNTING

plot.hap.score: Plot haplotype frequencies versus haplotype score statistics

print.hap.score: Print a hap.score object

qqfun: Quantile-comparison plots

qqunif: Q-Q plot for uniformly distributed random variable

read.ms.output: A utility function to read ms output

s2k: Statistics for 2 by K table

SNP: Functions for single nucleotide polymorphisms (SNPs)

tscc: Power calculation for two-stage case-control design

whscore: Whittemore-Halpern scores for allele-sharing

Files in this package

gap
gap/inst
gap/inst/CITATION
gap/inst/tests
gap/inst/tests/xls
gap/inst/tests/xls/BFDP.xls
gap/inst/tests/xls/FPRP.xls
gap/inst/tests/2ld
gap/inst/tests/2ld/2ld.c
gap/inst/tests/2ld/genotype.eh
gap/inst/tests/2ld/2ld.txt
gap/inst/tests/2ld/bench.bas
gap/inst/tests/2ld/kbyl.dat
gap/inst/tests/2ld/2by2.dat
gap/inst/tests/2ld/genotype.tab
gap/inst/tests/2ld/bench.dat
gap/inst/tests/2ld/genotype.dat
gap/inst/tests/ms
gap/inst/tests/ms/clms
gap/inst/tests/ms/www
gap/inst/tests/ms/rand2.c
gap/inst/tests/ms/rand1.c
gap/inst/tests/ms/msdoc.txt
gap/inst/tests/ms/ms.c
gap/inst/tests/ms/ms.h
gap/inst/tests/ms/streec.c
gap/inst/tests/sas
gap/inst/tests/sas/mtdt.sas
gap/inst/tests/sas/snphwe.sas
gap/inst/tests/sas/snphwe.sh
gap/inst/tests/sas/sas_snphwe.sas
gap/inst/tests/sas/snphwe.c
gap/inst/tests/sas/sasgwa.txt
gap/inst/tests/sas/metareg.sas
gap/inst/tests/sas/sasgwa.sas
gap/inst/tests/OpenMx
gap/inst/tests/OpenMx/install.R
gap/inst/tests/OpenMx/ACE.R
gap/inst/tests/misc
gap/inst/tests/misc/tidy.R
gap/inst/tests/misc/rm.c
gap/inst/tests/kinship
gap/inst/tests/kinship/nshd.dat
gap/inst/tests/kinship/solar.R
gap/inst/tests/kinship/pedtodot.sh
gap/inst/tests/kinship/ped7.pre
gap/inst/tests/kinship/werner.kin
gap/inst/tests/kinship/l51.R
gap/inst/tests/kinship/ped.1.3.pre
gap/inst/tests/kinship/kin.c
gap/inst/tests/kinship/gdef.h
gap/inst/tests/kinship/nghds.h
gap/inst/tests/kinship/gcta.R
gap/inst/tests/kinship/solar.sh
gap/inst/tests/kinship/bdsmatrix.R
gap/inst/tests/kinship/gcta.sh
gap/inst/tests/kinship/l51.sas
gap/inst/tests/kinship/gaw14.h
gap/inst/tests/kinship/readme
gap/inst/tests/kinship/werner.pre
gap/inst/tests/kinship/setup.R
gap/inst/tests/kinship/gaw14frq.c
gap/inst/tests/kinship/gaw14.c
gap/inst/tests/kinship/ped7.lop
gap/inst/tests/kinship/nshd.R
gap/inst/tests/kinship/h2.R
gap/inst/tests/kinship/kindrv.c
gap/inst/tests/comp.score
gap/inst/tests/comp.score/ibd_dist.out
gap/inst/tests/comp.score/linkloci.dat
gap/inst/tests/comp.score/gh.inp
gap/inst/tests/comp.score/pheno.dat
gap/inst/tests/comp.score/linkped.pre
gap/inst/tests/fehp
gap/inst/tests/fehp/aldh2.dat
gap/inst/tests/fehp/aldh2mm.par
gap/inst/tests/fehp/COPYRIGHT
gap/inst/tests/fehp/pfehp.h
gap/inst/tests/fehp/fpmp.doc
gap/inst/tests/fehp/makefile
gap/inst/tests/fehp/fpmp.h
gap/inst/tests/fehp/fpmp.pdf
gap/inst/tests/fehp/fehp.h
gap/inst/tests/fehp/fehp.c
gap/inst/tests/fehp/fpmp.c
gap/inst/tests/fehp/aldh2cc.par
gap/inst/tests/fehp/pfehp.c
gap/inst/tests/fehp/fpmp.tex
gap/inst/tests/chrsim
gap/inst/tests/chrsim/simulate.c
gap/inst/tests/chrsim/cs.dat
gap/inst/tests/chrsim/cs.c
gap/inst/tests/chrsim/cs.par
gap/inst/tests/haplo.stats
gap/inst/tests/haplo.stats/PD.R
gap/inst/tests/klem
gap/inst/tests/klem/SH2B1.R
gap/inst/tests/klem/SH2B1.txt
gap/inst/tests/ehp
gap/inst/tests/ehp/example.dat
gap/inst/tests/ehp/mm.par
gap/inst/tests/ehp/hla.par
gap/inst/tests/ehp/changes
gap/inst/tests/ehp/pm.c
gap/inst/tests/ehp/pmplus.c
gap/inst/tests/ehp/control.dat
gap/inst/tests/ehp/fehp.h
gap/inst/tests/ehp/ehplus.pas
gap/inst/tests/ehp/ehplus.dat
gap/inst/tests/ehp/hla.dat
gap/inst/tests/ehp/fehp.c
gap/inst/tests/ehp/Makefile.osf
gap/inst/tests/ehp/mm.dat
gap/inst/tests/ehp/example.par
gap/inst/tests/ehp/ehplush.c
gap/inst/tests/ehp/eh.c
gap/inst/tests/ehp/case.dat
gap/inst/tests/ehp/readme.txt
gap/inst/tests/ehp/htr.R
gap/inst/tests/ehp/pm.stm
gap/inst/tests/ehp/pm.doc
gap/inst/tests/ehp/eh.dat
gap/inst/tests/ehp/ehplush.pas
gap/inst/tests/ehp/ehplus.c
gap/inst/tests/references.txt
gap/inst/tests/twinan90
gap/inst/tests/twinan90/bwt.in
gap/inst/tests/twinan90/twinan90.for
gap/inst/tests/twinan90/twinan90.f
gap/inst/tests/twinan90/bwt.dat
gap/inst/tests/twinan90/twinan90.R
gap/inst/tests/twinan90/twinan90.Rd
gap/inst/tests/twinan90/mzdz.dat
gap/inst/tests/sim
gap/inst/tests/sim/ranlib
gap/inst/tests/sim/ranlib/Makefile
gap/inst/tests/sim/ranlib/src
gap/inst/tests/sim/ranlib/src/ranlib.c
gap/inst/tests/sim/ranlib/src/com.c
gap/inst/tests/sim/ranlib/README
gap/inst/tests/sim/ranlib/ranlib.h
gap/inst/tests/sim/ranlib/test
gap/inst/tests/sim/ranlib/test/tstmid.c
gap/inst/tests/sim/ranlib/test/sim.c
gap/inst/tests/sim/ranlib/test/tstbot.c
gap/inst/tests/sim/ranlib/test/genmul.c
gap/inst/tests/sim/ranlib/test/ranlib.h
gap/inst/tests/sim/ranlib/test/tstgmn.c
gap/inst/tests/sim/ranlib/doc
gap/inst/tests/sim/ranlib/doc/Basegen.c.doc
gap/inst/tests/sim/ranlib/doc/ranlib.c.fdoc
gap/inst/tests/sim/ranlib/doc/ranlib.c.chs
gap/inst/tests/sim/ranlib/linpack
gap/inst/tests/sim/ranlib/linpack/linpack.c
gap/inst/tests/sim/Makefile
gap/inst/tests/sim/src
gap/inst/tests/sim/src/simmain.c
gap/inst/tests/sim/src/getsize.c
gap/inst/tests/sim/src/outped.c
gap/inst/tests/sim/src/locprep.c
gap/inst/tests/sim/src/simped.c
gap/inst/tests/sim/src/diseq.c
gap/inst/tests/sim/src/nrutil.c
gap/inst/tests/sim/samples
gap/inst/tests/sim/samples/sim_ped.tst
gap/inst/tests/sim/samples/sim_loc.tst
gap/inst/tests/sim/samples/diseq.dat
gap/inst/tests/sim/samples/loc.tst
gap/inst/tests/sim/samples/ped.tst
gap/inst/tests/sim/samples/problem.dat
gap/inst/tests/sim/samples/diseq.loc
gap/inst/tests/sim/samples/ped.ped
gap/inst/tests/sim/doc
gap/inst/tests/sim/doc/sim.tex
gap/inst/tests/sim/doc/sim.pdf
gap/inst/tests/sim/include
gap/inst/tests/sim/include/nrutil.h
gap/inst/tests/sim/include/func.h
gap/inst/tests/sim/include/locus.h
gap/inst/tests/sim/include/person.h
gap/inst/tests/sim/include/sim.h
gap/inst/tests/README.txt
gap/inst/tests/hap
gap/inst/tests/hap/Makefile
gap/inst/tests/hap/hapfun.c
gap/inst/tests/hap/cline.c
gap/inst/tests/hap/test.dat
gap/inst/tests/hap/Makefile.vc
gap/inst/tests/hap/cline.h
gap/inst/tests/hap/4snps.4an
gap/inst/tests/hap/4snps.an
gap/inst/tests/hap/mia.c
gap/inst/tests/hap/4snps.dat
gap/inst/tests/hap/hap.txt
gap/inst/tests/hap/hap.c
gap/inst/tests/hap/hap.h
gap/inst/tests/stata
gap/inst/tests/stata/stata_snphwe.sh
gap/inst/tests/stata/connect_to_mysql.c
gap/inst/tests/stata/stata_snphwe.do
gap/inst/tests/stata/stata_snphwe.c
gap/inst/tests/stata/connect_to_mysql.do
gap/inst/tests/genecounting
gap/inst/tests/genecounting/gc.tex
gap/inst/tests/genecounting/gc.c
gap/inst/tests/genecounting/gcp.c
gap/inst/tests/genecounting/hla.par
gap/inst/tests/genecounting/changes
gap/inst/tests/genecounting/4snps.inp
gap/inst/tests/genecounting/gc.pdf
gap/inst/tests/genecounting/gc.txt
gap/inst/tests/genecounting/4snps.par
gap/inst/tests/genecounting/pgc.h
gap/inst/tests/genecounting/hla.dat
gap/inst/tests/genecounting/packing.lst
gap/inst/tests/genecounting/mao.dat
gap/inst/tests/genecounting/4snps.dat
gap/inst/tests/genecounting/pgc.c
gap/inst/tests/genecounting/gcx.c
gap/inst/tests/genecounting/mao.inp
gap/inst/tests/genecounting/4snps.4m
gap/inst/tests/no
gap/inst/doc
gap/inst/doc/gap.pdf
gap/inst/doc/pedtodot.R
gap/inst/doc/pedtodot.Rnw
gap/inst/doc/gap.Rnw
gap/inst/doc/pedtodot.pdf
gap/inst/doc/h2.Rnw
gap/inst/doc/h2.pdf
gap/inst/doc/rnews.pdf
gap/inst/doc/jss.Rnw
gap/inst/doc/gap.R
gap/inst/doc/jss.pdf
gap/inst/doc/rnews.Rnw
gap/src
gap/src/2ld.c
gap/src/2k.c
gap/src/cline.c
gap/src/kin.morgan.c
gap/src/makeped.c
gap/src/gdef.h
gap/src/nghds.h
gap/src/gif.c
gap/src/muvar.c
gap/src/pgc.h
gap/src/hwe.hardy.c
gap/src/cline.h
gap/src/whscore.c
gap/src/pfc.f
gap/src/gcontrol.c
gap/src/mia.c
gap/src/hap.c
gap/src/hap.h
gap/src/pgc.c
gap/src/gcx.c
gap/src/pfc.sim.f
gap/NAMESPACE
gap/demo
gap/demo/00Index
gap/demo/gap.R
gap/data
gap/data/mao.RData
gap/data/crohn.RData
gap/data/aldh2.rda
gap/data/hla.rda
gap/data/fsnps.RData
gap/data/PD.rda
gap/data/nep499.RData
gap/data/CDKN.RData
gap/data/mhtdata.RData
gap/data/mfblong.rda
gap/data/lukas.rda
gap/data/apoeapoc.rda
gap/data/fa.RData
gap/data/meyer.rda
gap/data/datalist
gap/data/l51.rda
gap/data/cf.RData
gap/data/hr1420.rda
gap/R
gap/R/onload.R gap/R/whscore.R gap/R/utils.R gap/R/masize.R gap/R/FPRP.R gap/R/pgc.R gap/R/metap.R gap/R/b2r.R gap/R/pedtodot.R gap/R/pfc.R gap/R/chow.test.R gap/R/hwe.R gap/R/hap.R gap/R/metareg.R gap/R/pfc.sim.R gap/R/mtdt.R gap/R/bt.R gap/R/comp.score.R gap/R/mhtplot2.R gap/R/hwe.cc.R gap/R/ccsize.R gap/R/asplot.R gap/R/gif.R gap/R/mia.R gap/R/muvar.R gap/R/gcontrol2.R gap/R/gc.em.R gap/R/mvmeta.R gap/R/gcontrol.R gap/R/mtdt2.R gap/R/tscc.R gap/R/hapfun.R gap/R/KCC.R gap/R/AE3.R gap/R/makeped.R gap/R/mhtplot.R gap/R/pbsize.R gap/R/hwe.hardy.R gap/R/read.ms.output.R gap/R/gcp.R gap/R/kin.morgan.R gap/R/htr.R gap/R/ESplot.R gap/R/s2k.R gap/R/BFDP.R gap/R/hap.score.R gap/R/qqunif.R gap/R/pbsize2.R gap/R/MCMCgrm.R gap/R/genecounting.R gap/R/hap.em.R gap/R/h2.R gap/R/qqfun.R gap/R/SNP.R gap/R/ab.R gap/R/fbsize.R gap/R/2ld.R
gap/vignettes
gap/vignettes/figures
gap/vignettes/figures/asplot.pdf
gap/vignettes/figures/qqunif.pdf
gap/vignettes/figures/lukas.pdf
gap/vignettes/figures/ESplot.pdf
gap/vignettes/figures/4w.pdf
gap/vignettes/figures/figure1.jpg
gap/vignettes/figures/mhtplot.png
gap/vignettes/4w.rda
gap/vignettes/gap.enl
gap/vignettes/jss.bib
gap/vignettes/pedtodot.Rnw
gap/vignettes/gap.Rnw
gap/vignettes/pedigrees.rda
gap/vignettes/gap.bib
gap/vignettes/h2.Rnw
gap/vignettes/results
gap/vignettes/results/gap_1.txt
gap/vignettes/results/gap_2.txt
gap/vignettes/results/kinship_1.txt
gap/vignettes/results/kinship_2.txt
gap/vignettes/jss.Rnw
gap/vignettes/pedigrees
gap/vignettes/pedigrees/dot2.pdf
gap/vignettes/pedigrees/fdp2.pdf
gap/vignettes/pedigrees/fdp3.pdf
gap/vignettes/pedigrees/dot1.pdf
gap/vignettes/pedigrees/fdp1.pdf
gap/vignettes/pedigrees/dot3.pdf
gap/vignettes/1-1-13.pdf
gap/vignettes/jsslogo.jpg
gap/vignettes/peddraw.pdf
gap/vignettes/rnews.Rnw
gap/MD5
gap/build
gap/build/vignette.rds
gap/DESCRIPTION
gap/ChangeLog
gap/man
gap/man/hap.Rd gap/man/pbsize.Rd gap/man/masize.Rd gap/man/gcontrol2.Rd gap/man/hwe.cc.Rd gap/man/gif.Rd gap/man/fbsize.Rd gap/man/hr1420.Rd gap/man/ESplot.Rd gap/man/BFDP.Rd gap/man/b2r.Rd gap/man/gc.em.Rd gap/man/hap.score.Rd gap/man/h2.Rd gap/man/hla.Rd gap/man/mvmeta.Rd gap/man/s2k.Rd gap/man/muvar.Rd gap/man/hwe.hardy.Rd gap/man/hwe.Rd gap/man/pfc.Rd gap/man/MCMCgrm.Rd gap/man/mao.Rd gap/man/fa.Rd gap/man/ccsize.Rd gap/man/crohn.Rd gap/man/apoeapoc.Rd gap/man/print.hap.score.Rd gap/man/mia.Rd gap/man/metareg.Rd gap/man/qqfun.Rd gap/man/AE3.Rd gap/man/mhtplot2.Rd gap/man/mhtplot.Rd gap/man/mfblong.Rd gap/man/ab.Rd gap/man/pedtodot.Rd gap/man/hap.em.Rd gap/man/metap.Rd gap/man/htr.Rd gap/man/LDkl.Rd gap/man/l51.Rd gap/man/lukas.Rd gap/man/asplot.Rd gap/man/qqunif.Rd gap/man/bt.Rd gap/man/aldh2.Rd gap/man/kin.morgan.Rd gap/man/pgc.Rd gap/man/chow.test.Rd gap/man/plot.hap.score.Rd gap/man/SNP.Rd gap/man/fsnps.Rd gap/man/mtdt2.Rd gap/man/gap-package.Rd gap/man/pbsize2.Rd gap/man/gap-internal.Rd gap/man/tscc.Rd gap/man/cf.Rd gap/man/gcontrol.Rd gap/man/CDKN.Rd gap/man/klem.Rd gap/man/FPRP.Rd gap/man/meyer.Rd gap/man/pfc.sim.Rd gap/man/mtdt.Rd gap/man/gcp.Rd gap/man/genecounting.Rd gap/man/nep499.Rd gap/man/read.ms.output.Rd gap/man/LD22.Rd gap/man/makeped.Rd gap/man/mhtdata.Rd gap/man/comp.score.Rd gap/man/PD.Rd gap/man/whscore.Rd
gap/INDEX

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