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.

Author
Jing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley
Date of publication
2015-06-06 08:56:06
Maintainer
Jing Hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>
License
GPL (>= 2)
Version
1.1-16
URLs

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