genetics: Population Genetics
Version 1.3.8.1

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.
Bioconductor views Genetics
Date of publication2013-09-03 12:06:28
MaintainerGregory Warnes <greg@warnes.net>
LicenseGPL
Version1.3.8.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("genetics")

Popular man pages

ci.balance: Experimental Function to Correct Confidence Intervals At or...
gregorius: Probability of Observing All Alleles with a Given Frequency...
HWE.chisq: Perform Chi-Square Test for Hardy-Weinberg Equilibrium
LD: Pairwise linkage disequilibrium between genetic markers.
locus: Create and Manipulate Locus, Gene, and Marker Objects
makeGenotypes: Convert columns in a dataframe to genotypes or haplotypes
order.genotype: Order/sort genotype/haplotype object
See all...

All man pages Function index File listing

Man pages

ci.balance: Experimental Function to Correct Confidence Intervals At or...
depreciated: Depreciated functions
diseq: Estimate or Compute Confidence Interval for the Single-Marker...
expectedGenotypes: Construct expected genotypes/haplotypes according to known...
genotype: Genotype or Haplotype Objects.
gregorius: Probability of Observing All Alleles with a Given Frequency...
groupGenotype: Group genotype values
homozygote: Extract Features of Genotype objects
HWE.chisq: Perform Chi-Square Test for Hardy-Weinberg Equilibrium
HWE.exact: Exact Test of Hardy-Weinberg Equilibrium for 2-Allele Markers
HWE.test: Estimate Disequilibrium and Test for Hardy-Weinberg...
LD: Pairwise linkage disequilibrium between genetic markers.
locus: Create and Manipulate Locus, Gene, and Marker Objects
makeGenotypes: Convert columns in a dataframe to genotypes or haplotypes
order.genotype: Order/sort genotype/haplotype object
plot.genotype: Plot genotype object
print.LD: Textual and graphical display of linkage disequilibrium (LD)...
summary.genotype: Allele and Genotype Frequency from a Genotype or Haplotype...
undocumented: Undocumented functions
write.pop.file: Create genetics data files

Functions

==.genotype Man page
==.haplotype Man page
HWE.chisq Man page Source code
HWE.chisq.genotype Man page Source code
HWE.exact Man page Source code
HWE.test Man page Source code
HWE.test.data.frame Man page Source code
HWE.test.genotype Man page Source code
LD Man page Source code
LD.data.frame Man page Source code
LD.genotype Man page Source code
LDplot Man page Source code
LDtable Man page Source code
[.genotype Man page
[.haplotype Man page
[<-.genotype Man page
[<-.haplotype Man page
\%in\% Man page
\%in\%.default Man page
\%in\%.genotype Man page
\%in\%.haplotype Man page
allele Man page Source code
allele.count Man page Source code
allele.count.2.genotype Man page Source code
allele.count.genotype Man page
allele.genotype Man page
allele.names Man page Man page Source code
as.character.gene Man page Source code
as.character.locus Man page Source code
as.character.marker Man page Source code
as.factor Man page Source code
as.factor.allele.genotype Man page Source code
as.factor.default Man page
as.factor.genotype Man page Source code
as.genotype Man page Source code
as.genotype.allele.count Man page Source code
as.genotype.character Man page Source code
as.genotype.default Man page Source code
as.genotype.factor Man page Source code
as.genotype.genotype Man page Source code
as.genotype.haplotype Man page Source code
as.genotype.table Man page Source code
as.haplotype Man page Source code
carrier Man page Source code
carrier.genotype Man page Source code
ci.balance Man page Source code
diseq Man page Source code
diseq.ci Man page Source code
diseq.genotype Man page Source code
diseq.table Man page Source code
expectedGenotypes Man page Source code
expectedHaplotypes Man page Source code
gene Man page Source code
gene<- Man page
geno.as.array Man page Source code
genotype Man page Source code
genotype2Allele Source code
genotype2Haplotype Source code
genotypeOrder Man page Source code
genotypeOrder<- Man page
getgene Man page
getlocus Man page Source code
getmarker Man page
gregorius Man page Source code
groupGenotype Man page Source code
hap Man page Source code
hapambig Man page Source code
hapenum Man page Source code
hapfreq Man page Source code
haplotype Man page Source code
hapmcmc Man page Source code
hapshuffle Man page Source code
heterozygote Man page Source code
heterozygote.genotype Man page Source code
homozygote Man page Source code
homozygote.genotype Man page Source code
is.gene Man page Source code
is.genotype Man page Source code
is.haplotype Man page Source code
is.locus Man page Source code
is.marker Man page Source code
locus Man page Source code
locus<- Man page
makeGenotypes Man page Source code
makeHaplotypes Man page Source code
marker Man page Source code
marker<- Man page
matchGenotype Source code
mknum Man page
mourant Man page Source code
nallele Man page Source code
onAttach Source code
order Man page Source code
order.default Source code
order.genotype Man page Source code
plot.LD.data.frame Man page Source code
plot.genotype Man page Source code
power.casectrl Man page Source code
power.casectrl.plot Source code
power.genotype.conti Source code
print.HWE.test Man page Source code
print.LD Man page Source code
print.LD.data.frame Man page Source code
print.allele.count Man page
print.allele.genotype Man page Source code
print.diseq Man page Source code
print.gene Man page Source code
print.genotype Man page Source code
print.locus Man page Source code
print.marker Man page Source code
print.summary.LD.data.frame Man page Source code
print.summary.genotype Man page Source code
pw Source code
shortsummary.genotype Man page Source code
simu.genotype.conti Source code
sort.genotype Man page Source code
summary.LD.data.frame Man page Source code
summary.genotype Man page Source code
write.marker.file Man page Source code
write.pedigree.file Man page Source code
write.pop.file Man page Source code

Files

TODO
inst
inst/NEWS
inst/ChangeLog
inst/doc
inst/doc/Rnews.sty
inst/doc/example.R
inst/doc/genetics_article.pdf
inst/doc/LD.pdf
inst/doc/example_data.csv
inst/doc/genetics_article.tex
inst/doc/make_example_data.R
tests
tests/makeGenotype_with_sep.R
tests/test.NA.R
tests/ci.balance.R
NAMESPACE
NEWS
data
data/gregorius.rda
R
R/plot.genotype.R
R/groupGenotype.R
R/locus.R
R/plot.LD.R
R/LD.R
R/write.pedigree.file.R
R/power.casectl.R
R/hapmcmc.R
R/HWE.test.data.frame.R
R/print.LD.R
R/HWE.test.R
R/ci.balance.R
R/write.pop.file.R
R/genotype.R
R/HWE.exact.R
R/HWE.chisq.R
R/diseq.R
R/makeGenotypes.R
R/expectedGenotypes.R
R/order.genotype.R
R/gregorius.R
R/summary.genotype.R
R/zzz.R
R/power.casectl.plot.R
MD5
DESCRIPTION
ChangeLog
man
man/expectedGenotypes.Rd
man/LD.Rd
man/HWE.exact.Rd
man/undocumented.Rd
man/ci.balance.Rd
man/groupGenotype.Rd
man/write.pop.file.Rd
man/HWE.chisq.Rd
man/genotype.Rd
man/print.LD.Rd
man/summary.genotype.Rd
man/makeGenotypes.Rd
man/depreciated.Rd
man/order.genotype.Rd
man/diseq.Rd
man/homozygote.Rd
man/gregorius.Rd
man/plot.genotype.Rd
man/HWE.test.Rd
man/locus.Rd
.Rinstignore
genetics documentation built on May 19, 2017, 8:33 a.m.

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