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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, ...

Functions (20)

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 Equilibrium

LD

Pairwise linkage disequilibrium between genetic markers.

ci.balance

Experimental Function to Correct Confidence Intervals At or Near Boundaries of the Parameter Space by 'Sliding' the Interval on the Quantile Scale.

depreciated

Depreciated functions

diseq

Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium

expectedGenotypes

Construct expected genotypes/haplotypes according to known allele variants

genotype

Genotype or Haplotype Objects.

gregorius

Probability of Observing All Alleles with a Given Frequency in a Sample of a Specified Size.

groupGenotype

Group genotype values

homozygote

Extract Features of Genotype objects

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) objects

summary.genotype

Allele and Genotype Frequency from a Genotype or Haplotype Object

undocumented

Undocumented functions

write.pop.file

Create genetics data files

genetics

Population Genetics

v1.3.8.1.3
GPL
Authors
Gregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch, and Michael Man.
Initial release
2012-11-26

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