genetics: Population Genetics

Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...

AuthorGregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch, and Michael Man.
Date of publication2013-09-03 12:06:28
MaintainerGregory Warnes <greg@warnes.net>
LicenseGPL
Version1.3.8.1

View on CRAN

Functions

allele Man page
allele.count Man page
allele.count.2.genotype Man page
allele.count.genotype Man page
allele.genotype Man page
allele.names Man page
allele.names Man page
as.character.gene Man page
as.character.locus Man page
as.character.marker Man page
as.factor Man page
as.factor.allele.genotype Man page
as.factor.default Man page
as.factor.genotype Man page
as.genotype Man page
as.genotype.allele.count Man page
as.genotype.character Man page
as.genotype.default Man page
as.genotype.factor Man page
as.genotype.genotype Man page
as.genotype.haplotype Man page
as.genotype.table Man page
as.haplotype Man page
carrier Man page
carrier.genotype Man page
ci.balance Man page
diseq Man page
diseq.ci Man page
diseq.genotype Man page
diseq.table Man page
expectedGenotypes Man page
expectedHaplotypes Man page
gene Man page
gene<- Man page
geno.as.array Man page
genotype Man page
==.genotype Man page
[<-.genotype Man page
[.genotype Man page
genotypeOrder Man page
genotypeOrder<- Man page
getgene Man page
getlocus Man page
getmarker Man page
gregorius Man page
groupGenotype Man page
hap Man page
hapambig Man page
hapenum Man page
hapfreq Man page
haplotype Man page
==.haplotype Man page
[<-.haplotype Man page
[.haplotype Man page
hapmcmc Man page
hapshuffle Man page
heterozygote Man page
heterozygote.genotype Man page
homozygote Man page
homozygote.genotype Man page
HWE.chisq Man page
HWE.chisq.genotype Man page
HWE.exact Man page
HWE.test Man page
HWE.test.data.frame Man page
HWE.test.genotype Man page
\%in\% Man page
\%in\%.default Man page
\%in\%.genotype Man page
\%in\%.haplotype Man page
is.gene Man page
is.genotype Man page
is.haplotype Man page
is.locus Man page
is.marker Man page
LD Man page
LD.data.frame Man page
LD.genotype Man page
LDplot Man page
LDtable Man page
locus Man page
locus<- Man page
makeGenotypes Man page
makeHaplotypes Man page
marker Man page
marker<- Man page
mknum Man page
mourant Man page
nallele Man page
order Man page
order.genotype Man page
plot.genotype Man page
plot.LD.data.frame Man page
power.casectrl Man page
print.allele.count Man page
print.allele.genotype Man page
print.diseq Man page
print.gene Man page
print.genotype Man page
print.HWE.test Man page
print.LD Man page
print.LD.data.frame Man page
print.locus Man page
print.marker Man page
print.summary.genotype Man page
print.summary.LD.data.frame Man page
shortsummary.genotype Man page
sort.genotype Man page
summary.genotype Man page
summary.LD.data.frame Man page
write.marker.file Man page
write.pedigree.file Man page
write.pop.file Man page

Files

genetics
genetics/TODO
genetics/inst
genetics/inst/NEWS
genetics/inst/ChangeLog
genetics/inst/doc
genetics/inst/doc/Rnews.sty
genetics/inst/doc/example.R
genetics/inst/doc/genetics_article.pdf
genetics/inst/doc/LD.pdf
genetics/inst/doc/example_data.csv
genetics/inst/doc/genetics_article.tex
genetics/inst/doc/make_example_data.R
genetics/tests
genetics/tests/makeGenotype_with_sep.R
genetics/tests/test.NA.R
genetics/tests/ci.balance.R
genetics/NAMESPACE
genetics/NEWS
genetics/data
genetics/data/gregorius.rda
genetics/R
genetics/R/plot.genotype.R genetics/R/groupGenotype.R genetics/R/locus.R genetics/R/plot.LD.R genetics/R/LD.R genetics/R/write.pedigree.file.R genetics/R/power.casectl.R genetics/R/hapmcmc.R genetics/R/HWE.test.data.frame.R genetics/R/print.LD.R genetics/R/HWE.test.R genetics/R/ci.balance.R genetics/R/write.pop.file.R genetics/R/genotype.R genetics/R/HWE.exact.R genetics/R/HWE.chisq.R genetics/R/diseq.R genetics/R/makeGenotypes.R genetics/R/expectedGenotypes.R genetics/R/order.genotype.R genetics/R/gregorius.R genetics/R/summary.genotype.R genetics/R/zzz.R genetics/R/power.casectl.plot.R
genetics/MD5
genetics/DESCRIPTION
genetics/ChangeLog
genetics/man
genetics/man/expectedGenotypes.Rd genetics/man/LD.Rd genetics/man/HWE.exact.Rd genetics/man/undocumented.Rd genetics/man/ci.balance.Rd genetics/man/groupGenotype.Rd genetics/man/write.pop.file.Rd genetics/man/HWE.chisq.Rd genetics/man/genotype.Rd genetics/man/print.LD.Rd genetics/man/summary.genotype.Rd genetics/man/makeGenotypes.Rd genetics/man/depreciated.Rd genetics/man/order.genotype.Rd genetics/man/diseq.Rd genetics/man/homozygote.Rd genetics/man/gregorius.Rd genetics/man/plot.genotype.Rd genetics/man/HWE.test.Rd genetics/man/locus.Rd
genetics/.Rinstignore

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