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.

Install the latest version of this package by entering the following in R:
install.packages("gap")
AuthorJing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley
Date of publication2017-04-19 11:10:23 UTC
MaintainerJing Hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>
LicenseGPL (>= 2)
Version1.1-17
http://people.ds.cam.ac.uk/jhz22/

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

Functions

a2g Man page
ab Man page
AE3 Man page
aldh2 Man page
allele.recode Man page
apoeapoc Man page
asplot Man page
b2r Man page
BFDP Man page
bt Man page
ccsize Man page
CDKN Man page
CDKNgenes Man page
CDKNlocus Man page
CDKNmap Man page
cf Man page
chow.test Man page
ci Man page
comp.score Man page
cov.invlogit Man page
Cox.est Man page
Cox.T Man page
crohn Man page
Dev Man page
Dev.est Man page
DevH0dominant Man page
DevH0dominant.est Man page
DevH0recessive Man page
DevH0recessive.est Man page
DevHaGdominant Man page
DevHaGdominant.est Man page
DevHaGrecessive Man page
DevHaGrecessive.est Man page
DevHa.recessive Man page
DevHa.recessive.est Man page
ESplot Man page
ExpN.recessiveH0 Man page
ExpN.recessiveHa Man page
fa Man page
fbsize Man page
FPRP Man page
fsnps Man page
g2a Man page
g2a.c Man page
gap Man page
gap-package Man page
gc.control Man page
gc.em Man page
gcode Man page
gcontrol Man page
gcontrol2 Man page
gcp Man page
genecounting Man page
geno.p Man page
geno.recode Man page
getb1star Man page
getPTE Man page
gif Man page
grec2g Man page
h2 Man page
h2G Man page
h2GE Man page
h2l Man page
hap Man page
hap.control Man page
HapDesign Man page
hap.em Man page
HapFreqSE Man page
hap.score Man page
hap.score.glm Man page
hap.score.podds Man page
hla Man page
hmht.control Man page
hr1420 Man page
htr Man page
hw Man page
hwe Man page
hwe.cc Man page
hwe.hardy Man page
invlogit Man page
is.miss Man page
k Man page
KCC Man page
kin.morgan Man page
klem Man page
l51 Man page
LD22 Man page
LDkl Man page
logit Man page
lukas Man page
m2plem Man page
makeped Man page
mao Man page
masize Man page
MCMCgrm Man page
metap Man page
metareg Man page
meyer Man page
mfblong Man page
mht.control Man page
mhtdata Man page
mhtplot Man page
mhtplot2 Man page
mia Man page
micombine Man page
mtdt Man page
mtdt2 Man page
muvar Man page
mvmeta Man page
nep499 Man page
PARn Man page
pbsize Man page
pbsize2 Man page
PD Man page
pedtodot Man page
pfc Man page
pfc.sim Man page
pgc Man page
plem2m Man page
plot.hap.score Man page
pm Man page
pmplus Man page
print.hap.score Man page
qqfun Man page
qqunif Man page
ReadGRM Man page
ReadGRMBin Man page
ReadGRMPCA Man page
ReadGRMPLINK Man page
read.ms.output Man page
revhap Man page
revhap.i Man page
s2k Man page
se.exp Man page
se.invlogit Man page
SNP Man page
snp.ES Man page
snp.HWE Man page
snp.PAR Man page
solve_skol Man page
toETDT Man page
tscc Man page
ungcode Man page
VR Man page
whscore Man page
WriteGRM Man page
WriteGRMBin Man page
WriteGRMSAS Man page
x2 Man page
z Man page

Files

inst
inst/CITATION
inst/tests
inst/tests/xls
inst/tests/xls/BFDP.xls
inst/tests/xls/FPRP.xls
inst/tests/2ld
inst/tests/2ld/2ld.c
inst/tests/2ld/genotype.eh
inst/tests/2ld/2ld.txt
inst/tests/2ld/bench.bas
inst/tests/2ld/kbyl.dat
inst/tests/2ld/2by2.dat
inst/tests/2ld/genotype.tab
inst/tests/2ld/bench.dat
inst/tests/2ld/genotype.dat
inst/tests/ms
inst/tests/ms/clms
inst/tests/ms/www
inst/tests/ms/rand2.c
inst/tests/ms/rand1.c
inst/tests/ms/msdoc.txt
inst/tests/ms/ms.c
inst/tests/ms/ms.h
inst/tests/ms/streec.c
inst/tests/sas
inst/tests/sas/mtdt.sas
inst/tests/sas/snphwe.sas
inst/tests/sas/snphwe.sh
inst/tests/sas/sas_snphwe.sas
inst/tests/sas/snphwe.c
inst/tests/sas/sasgwa.txt
inst/tests/sas/metareg.sas
inst/tests/sas/sasgwa.sas
inst/tests/OpenMx
inst/tests/OpenMx/install.R inst/tests/OpenMx/ACE.R
inst/tests/misc
inst/tests/misc/tidy.R
inst/tests/misc/rm.c
inst/tests/kinship
inst/tests/kinship/nshd.dat
inst/tests/kinship/solar.R
inst/tests/kinship/pedtodot.sh
inst/tests/kinship/ped7.pre
inst/tests/kinship/werner.kin
inst/tests/kinship/l51.R
inst/tests/kinship/ped.1.3.pre
inst/tests/kinship/kin.c
inst/tests/kinship/gdef.h
inst/tests/kinship/nghds.h
inst/tests/kinship/gcta.R
inst/tests/kinship/solar.sh
inst/tests/kinship/bdsmatrix.R
inst/tests/kinship/gcta.sh
inst/tests/kinship/l51.sas
inst/tests/kinship/gaw14.h
inst/tests/kinship/readme
inst/tests/kinship/werner.pre
inst/tests/kinship/setup.R
inst/tests/kinship/gaw14frq.c
inst/tests/kinship/gaw14.c
inst/tests/kinship/ped7.lop
inst/tests/kinship/nshd.R inst/tests/kinship/h2.R
inst/tests/kinship/kindrv.c
inst/tests/comp.score
inst/tests/comp.score/ibd_dist.out
inst/tests/comp.score/linkloci.dat
inst/tests/comp.score/gh.inp
inst/tests/comp.score/pheno.dat
inst/tests/comp.score/linkped.pre
inst/tests/fehp
inst/tests/fehp/aldh2.dat
inst/tests/fehp/aldh2mm.par
inst/tests/fehp/COPYRIGHT
inst/tests/fehp/pfehp.h
inst/tests/fehp/fpmp.doc
inst/tests/fehp/makefile
inst/tests/fehp/fpmp.h
inst/tests/fehp/fpmp.pdf
inst/tests/fehp/fehp.h
inst/tests/fehp/fehp.c
inst/tests/fehp/fpmp.c
inst/tests/fehp/aldh2cc.par
inst/tests/fehp/pfehp.c
inst/tests/fehp/fpmp.tex
inst/tests/chrsim
inst/tests/chrsim/simulate.c
inst/tests/chrsim/cs.dat
inst/tests/chrsim/cs.c
inst/tests/chrsim/cs.par
inst/tests/R
inst/tests/R/test_data.rda
inst/tests/R/R2.R inst/tests/R/MR.R inst/tests/R/renum.R
inst/tests/haplo.stats
inst/tests/haplo.stats/PD.R
inst/tests/klem
inst/tests/klem/SH2B1.R
inst/tests/klem/SH2B1.txt
inst/tests/ehp
inst/tests/ehp/example.dat
inst/tests/ehp/mm.par
inst/tests/ehp/hla.par
inst/tests/ehp/changes
inst/tests/ehp/pm.c
inst/tests/ehp/pmplus.c
inst/tests/ehp/control.dat
inst/tests/ehp/fehp.h
inst/tests/ehp/ehplus.pas
inst/tests/ehp/ehplus.dat
inst/tests/ehp/hla.dat
inst/tests/ehp/fehp.c
inst/tests/ehp/Makefile.osf
inst/tests/ehp/mm.dat
inst/tests/ehp/example.par
inst/tests/ehp/ehplush.c
inst/tests/ehp/eh.c
inst/tests/ehp/case.dat
inst/tests/ehp/readme.txt
inst/tests/ehp/htr.R
inst/tests/ehp/pm.stm
inst/tests/ehp/pm.doc
inst/tests/ehp/eh.dat
inst/tests/ehp/ehplush.pas
inst/tests/ehp/ehplus.c
inst/tests/h2
inst/tests/h2/map.csv
inst/tests/h2/R2.R
inst/tests/h2/R2.do
inst/tests/h2/ddjack.sh
inst/tests/h2/map.R inst/tests/h2/mvmeta.R
inst/tests/h2/ddjack.do
inst/tests/h2/figures.R inst/tests/h2/ggmap.R
inst/tests/h2/bootjack.sas
inst/tests/h2/mvmeta.do
inst/tests/h2/h2GE_bmi.R
inst/tests/references.txt
inst/tests/twinan90
inst/tests/twinan90/bwt.in
inst/tests/twinan90/twinan90.for
inst/tests/twinan90/twinan90.f
inst/tests/twinan90/bwt.dat
inst/tests/twinan90/twinan90.R
inst/tests/twinan90/twinan90.Rd
inst/tests/twinan90/mzdz.dat
inst/tests/sim
inst/tests/sim/ranlib
inst/tests/sim/ranlib/Makefile
inst/tests/sim/ranlib/src
inst/tests/sim/ranlib/src/ranlib.c
inst/tests/sim/ranlib/src/com.c
inst/tests/sim/ranlib/README
inst/tests/sim/ranlib/ranlib.h
inst/tests/sim/ranlib/test
inst/tests/sim/ranlib/test/tstmid.c
inst/tests/sim/ranlib/test/sim.c
inst/tests/sim/ranlib/test/tstbot.c
inst/tests/sim/ranlib/test/genmul.c
inst/tests/sim/ranlib/test/ranlib.h
inst/tests/sim/ranlib/test/tstgmn.c
inst/tests/sim/ranlib/doc
inst/tests/sim/ranlib/doc/Basegen.c.doc
inst/tests/sim/ranlib/doc/ranlib.c.fdoc
inst/tests/sim/ranlib/doc/ranlib.c.chs
inst/tests/sim/ranlib/linpack
inst/tests/sim/ranlib/linpack/linpack.c
inst/tests/sim/Makefile
inst/tests/sim/src
inst/tests/sim/src/simmain.c
inst/tests/sim/src/getsize.c
inst/tests/sim/src/outped.c
inst/tests/sim/src/locprep.c
inst/tests/sim/src/simped.c
inst/tests/sim/src/diseq.c
inst/tests/sim/src/nrutil.c
inst/tests/sim/samples
inst/tests/sim/samples/sim_ped.tst
inst/tests/sim/samples/sim_loc.tst
inst/tests/sim/samples/diseq.dat
inst/tests/sim/samples/loc.tst
inst/tests/sim/samples/ped.tst
inst/tests/sim/samples/problem.dat
inst/tests/sim/samples/diseq.loc
inst/tests/sim/samples/ped.ped
inst/tests/sim/doc
inst/tests/sim/doc/sim.tex
inst/tests/sim/doc/sim.pdf
inst/tests/sim/include
inst/tests/sim/include/nrutil.h
inst/tests/sim/include/func.h
inst/tests/sim/include/locus.h
inst/tests/sim/include/person.h
inst/tests/sim/include/sim.h
inst/tests/README.txt
inst/tests/hap
inst/tests/hap/Makefile
inst/tests/hap/hapfun.c
inst/tests/hap/cline.c
inst/tests/hap/test.dat
inst/tests/hap/Makefile.vc
inst/tests/hap/cline.h
inst/tests/hap/4snps.4an
inst/tests/hap/4snps.an
inst/tests/hap/mia.c
inst/tests/hap/4snps.dat
inst/tests/hap/hap.txt
inst/tests/hap/hap.c
inst/tests/hap/hap.h
inst/tests/stata
inst/tests/stata/stata_snphwe.sh
inst/tests/stata/connect_to_mysql.c
inst/tests/stata/stata_snphwe.do
inst/tests/stata/stata_snphwe.c
inst/tests/stata/connect_to_mysql.do
inst/tests/genecounting
inst/tests/genecounting/gc.tex
inst/tests/genecounting/gc.c
inst/tests/genecounting/gcp.c
inst/tests/genecounting/hla.par
inst/tests/genecounting/changes
inst/tests/genecounting/4snps.inp
inst/tests/genecounting/gc.pdf
inst/tests/genecounting/gc.txt
inst/tests/genecounting/4snps.par
inst/tests/genecounting/pgc.h
inst/tests/genecounting/hla.dat
inst/tests/genecounting/packing.lst
inst/tests/genecounting/mao.dat
inst/tests/genecounting/4snps.dat
inst/tests/genecounting/pgc.c
inst/tests/genecounting/gcx.c
inst/tests/genecounting/mao.inp
inst/tests/genecounting/4snps.4m
inst/tests/no
inst/doc
inst/doc/gap.pdf
inst/doc/pedtodot.R
inst/doc/pedtodot.Rnw
inst/doc/gap.Rnw
inst/doc/pedtodot.pdf
inst/doc/h2.Rnw
inst/doc/h2.pdf
inst/doc/rnews.pdf
inst/doc/jss.Rnw
inst/doc/gap.R
inst/doc/jss.pdf
inst/doc/rnews.Rnw
src
src/2ld.c
src/2k.c
src/package_native_routine_registration_skeleton.c
src/cline.c
src/kin.morgan.c
src/hap_c.c
src/gdef.h
src/nghds.h
src/gcontrol_c.c
src/muvar.c
src/pgc.h
src/makeped_c.c
src/hwe.hardy.c
src/cline.h
src/whscore.c
src/pfc.f
src/mia.c
src/hap.h
src/gcx.c
src/gif_c.c
src/pgc_c.c
src/pfc.sim.f
NAMESPACE
demo
demo/00Index
demo/gap.R
data
data/mao.RData
data/crohn.RData
data/aldh2.rda
data/hla.rda
data/fsnps.RData
data/PD.rda
data/nep499.RData
data/CDKN.RData
data/mhtdata.RData
data/mfblong.rda
data/lukas.rda
data/apoeapoc.rda
data/fa.RData
data/meyer.rda
data/datalist
data/l51.rda
data/cf.RData
data/hr1420.rda
R
R/onload.R R/whscore.R R/utils.R R/masize.R R/FPRP.R R/pgc.R R/metap.R R/b2r.R R/pedtodot.R R/pfc.R R/chow.test.R R/hwe.R R/hap.R R/metareg.R R/pfc.sim.R R/mtdt.R R/bt.R R/comp.score.R R/mhtplot2.R R/hwe.cc.R R/ccsize.R R/asplot.R R/gif.R R/mia.R R/muvar.R R/gcontrol2.R R/gc.em.R R/mvmeta.R R/gcontrol.R R/mtdt2.R R/tscc.R R/hapfun.R R/KCC.R R/AE3.R R/makeped.R R/mhtplot.R R/pbsize.R R/hwe.hardy.R R/read.ms.output.R R/gcp.R R/kin.morgan.R R/htr.R R/ESplot.R R/s2k.R R/BFDP.R R/hap.score.R R/qqunif.R R/pbsize2.R R/MCMCgrm.R R/genecounting.R R/hap.em.R R/h2.R R/qqfun.R R/SNP.R R/ab.R R/fbsize.R R/2ld.R
vignettes
vignettes/figures
vignettes/figures/asplot.pdf
vignettes/figures/qqunif.pdf
vignettes/figures/lukas.pdf
vignettes/figures/ESplot.pdf
vignettes/figures/4w.pdf
vignettes/figures/figure1.jpg
vignettes/figures/mhtplot.png
vignettes/4w.rda
vignettes/gap.enl
vignettes/jss.bib
vignettes/pedtodot.Rnw
vignettes/gap.Rnw
vignettes/pedigrees.rda
vignettes/gap.bib
vignettes/h2.Rnw
vignettes/results
vignettes/results/gap_1.txt
vignettes/results/gap_2.txt
vignettes/results/kinship_1.txt
vignettes/results/kinship_2.txt
vignettes/jss.Rnw
vignettes/pedigrees
vignettes/pedigrees/dot2.pdf
vignettes/pedigrees/fdp2.pdf
vignettes/pedigrees/fdp3.pdf
vignettes/pedigrees/dot1.pdf
vignettes/pedigrees/fdp1.pdf
vignettes/pedigrees/dot3.pdf
vignettes/1-1-13.pdf
vignettes/jsslogo.jpg
vignettes/peddraw.pdf
vignettes/rnews.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/hap.Rd man/pbsize.Rd man/masize.Rd man/gcontrol2.Rd man/hwe.cc.Rd man/gif.Rd man/fbsize.Rd man/hr1420.Rd man/ESplot.Rd man/BFDP.Rd man/b2r.Rd man/gc.em.Rd man/hap.score.Rd man/h2.Rd man/hla.Rd man/mvmeta.Rd man/s2k.Rd man/muvar.Rd man/hwe.hardy.Rd man/hwe.Rd man/pfc.Rd man/MCMCgrm.Rd man/mao.Rd man/fa.Rd man/ccsize.Rd man/crohn.Rd man/apoeapoc.Rd man/print.hap.score.Rd man/mia.Rd man/metareg.Rd man/qqfun.Rd man/AE3.Rd man/mhtplot2.Rd man/mhtplot.Rd man/mfblong.Rd man/ab.Rd man/pedtodot.Rd man/hap.em.Rd man/metap.Rd man/htr.Rd man/LDkl.Rd man/l51.Rd man/lukas.Rd man/asplot.Rd man/qqunif.Rd man/bt.Rd man/aldh2.Rd man/kin.morgan.Rd man/pgc.Rd man/chow.test.Rd man/plot.hap.score.Rd man/SNP.Rd man/fsnps.Rd man/mtdt2.Rd man/gap-package.Rd man/pbsize2.Rd man/gap-internal.Rd man/tscc.Rd man/cf.Rd man/gcontrol.Rd man/CDKN.Rd man/klem.Rd man/FPRP.Rd man/meyer.Rd man/pfc.sim.Rd man/mtdt.Rd man/gcp.Rd man/genecounting.Rd man/nep499.Rd man/read.ms.output.Rd man/LD22.Rd man/makeped.Rd man/mhtdata.Rd man/comp.score.Rd man/PD.Rd man/whscore.Rd
INDEX
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