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genetics (version 1.3.8.1.3)

Population Genetics

Description

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, ...

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Version

Install

install.packages('genetics')

Monthly Downloads

3,368

Version

1.3.8.1.3

License

GPL

Maintainer

the of this package were written by Gregory R. Warnes

Last Published

March 1st, 2021

Functions in genetics (1.3.8.1.3)

Genotype or Haplotype Objects.

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

Exact Test of Hardy-Weinberg Equilibrium for 2-Allele Markers

Estimate Disequilibrium and Test for Hardy-Weinberg Equilibrium

Depreciated functions

Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium

Pairwise linkage disequilibrium between genetic markers.

Perform Chi-Square Test for Hardy-Weinberg Equilibrium

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

Undocumented functions

expectedGenotypes

Construct expected genotypes/haplotypes according to known allele variants

Order/sort genotype/haplotype object

Extract Features of Genotype objects

Group genotype values

Plot genotype object

Create genetics data files

summary.genotype

Allele and Genotype Frequency from a Genotype or Haplotype Object

Textual and graphical display of linkage disequilibrium (LD) objects

Create and Manipulate Locus, Gene, and Marker Objects

Convert columns in a dataframe to genotypes or haplotypes