genetics v1.


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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 in genetics

Name Description
HWE.test Estimate Disequilibrium and Test for Hardy-Weinberg Equilibrium
plot.genotype Plot genotype object
HWE.chisq Perform Chi-Square Test for Hardy-Weinberg Equilibrium
HWE.exact Exact Test of Hardy-Weinberg Equilibrium for 2-Allele Markers
print.LD Textual and graphical display of linkage disequilibrium (LD) objects
summary.genotype Allele and Genotype Frequency from a Genotype or Haplotype Object
diseq Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium
expectedGenotypes Construct expected genotypes/haplotypes according to known allele variants
undocumented Undocumented functions
write.pop.file Create genetics data files
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
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
locus Create and Manipulate Locus, Gene, and Marker Objects
makeGenotypes Convert columns in a dataframe to genotypes or haplotypes
LD Pairwise linkage disequilibrium between genetic markers.
order.genotype Order/sort genotype/haplotype object
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Date 2012-11-26
biocViews Genetics
License GPL
Packaged 2019-04-21 11:05:10 UTC; ripley
Repository CRAN
Date/Publication 2019-04-22 06:57:07 UTC
NeedsCompilation no

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