genetics: Population Genetics

Share:

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, ...

Author
Gregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch, and Michael Man.
Date of publication
2013-09-03 12:06:28
Maintainer
Gregory Warnes <greg@warnes.net>
License
GPL
Version
1.3.8.1

View on CRAN

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

Files in this package

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