R: Population Genetics

# Population Genetics

## Documentation for package ‘genetics’ version 1.3.8.1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A C D E G H I L M N O P S W misc

## -- A --

allele | Extract Features of Genotype objects
allele.count | Extract Features of Genotype objects
allele.count.2.genotype | Undocumented functions
allele.count.genotype | Genotype or Haplotype Objects.
allele.names | Extract Features of Genotype objects
as.character.gene | Create and Manipulate Locus, Gene, and Marker Objects
as.character.locus | Create and Manipulate Locus, Gene, and Marker Objects
as.character.marker | Create and Manipulate Locus, Gene, and Marker Objects
as.factor | Undocumented functions
as.factor.allele.genotype | Undocumented functions
as.factor.default | Undocumented functions
as.factor.genotype | Undocumented functions
as.genotype | Genotype or Haplotype Objects.
as.genotype.allele.count | Genotype or Haplotype Objects.
as.genotype.character | Genotype or Haplotype Objects.
as.genotype.default | Genotype or Haplotype Objects.
as.genotype.factor | Genotype or Haplotype Objects.
as.genotype.genotype | Genotype or Haplotype Objects.
as.genotype.haplotype | Genotype or Haplotype Objects.
as.genotype.table | Genotype or Haplotype Objects.
as.haplotype | Genotype or Haplotype Objects.

## -- C --

carrier | Extract Features of Genotype objects
carrier.genotype | 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.

## -- D --

diseq | Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium
diseq.ci | Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium
diseq.genotype | Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium
diseq.table | Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium

## -- E --

expectedGenotypes | Construct expected genotypes/haplotypes according to known allele variants
expectedHaplotypes | Construct expected genotypes/haplotypes according to known allele variants

## -- G --

gene | Create and Manipulate Locus, Gene, and Marker Objects
gene<- | Create and Manipulate Locus, Gene, and Marker Objects
geno.as.array | Undocumented functions
genotype | Genotype or Haplotype Objects.
genotypeOrder | Order/sort genotype/haplotype object
genotypeOrder<- | Order/sort genotype/haplotype object
getgene | Create and Manipulate Locus, Gene, and Marker Objects
getlocus | Create and Manipulate Locus, Gene, and Marker Objects
getmarker | Create and Manipulate Locus, Gene, and Marker Objects
gregorius | Probability of Observing All Alleles with a Given Frequency in a Sample of a Specified Size.
groupGenotype | Group genotype values

## -- H --

hap | Undocumented functions
hapambig | Undocumented functions
hapenum | Undocumented functions
hapfreq | Undocumented functions
haplotype | Genotype or Haplotype Objects.
hapmcmc | Undocumented functions
hapshuffle | Undocumented functions
heterozygote | Extract Features of Genotype objects
heterozygote.genotype | Genotype or Haplotype Objects.
homozygote | Extract Features of Genotype objects
homozygote.genotype | Genotype or Haplotype Objects.
HWE.chisq | Perform Chi-Square Test for Hardy-Weinberg Equilibrium
HWE.chisq.genotype | 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
HWE.test.data.frame | Estimate Disequilibrium and Test for Hardy-Weinberg Equilibrium
HWE.test.genotype | Estimate Disequilibrium and Test for Hardy-Weinberg Equilibrium

## -- I --

is.gene | Create and Manipulate Locus, Gene, and Marker Objects
is.genotype | Genotype or Haplotype Objects.
is.haplotype | Genotype or Haplotype Objects.
is.locus | Create and Manipulate Locus, Gene, and Marker Objects
is.marker | Create and Manipulate Locus, Gene, and Marker Objects

## -- L --

LD | Pairwise linkage disequilibrium between genetic markers.
LD.data.frame | Pairwise linkage disequilibrium between genetic markers.
LD.genotype | Pairwise linkage disequilibrium between genetic markers.
LDplot | Textual and graphical display of linkage disequilibrium (LD) objects
LDtable | Textual and graphical display of linkage disequilibrium (LD) objects
locus | Create and Manipulate Locus, Gene, and Marker Objects
locus<- | Create and Manipulate Locus, Gene, and Marker Objects

## -- M --

makeGenotypes | Convert columns in a dataframe to genotypes or haplotypes
makeHaplotypes | Convert columns in a dataframe to genotypes or haplotypes
marker | Create and Manipulate Locus, Gene, and Marker Objects
marker<- | Create and Manipulate Locus, Gene, and Marker Objects
mknum | Undocumented functions
mourant | Undocumented functions

## -- N --

nallele | Genotype or Haplotype Objects.

## -- O --

order | Order/sort genotype/haplotype object
order.genotype | Order/sort genotype/haplotype object

## -- P --

plot.genotype | Plot genotype object
plot.LD.data.frame | Textual and graphical display of linkage disequilibrium (LD) objects
power.casectrl | Depreciated functions
print.allele.count | Genotype or Haplotype Objects.
print.allele.genotype | Genotype or Haplotype Objects.
print.diseq | Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium
print.gene | Create and Manipulate Locus, Gene, and Marker Objects
print.genotype | Genotype or Haplotype Objects.
print.HWE.test | Estimate Disequilibrium and Test for Hardy-Weinberg Equilibrium
print.LD | Textual and graphical display of linkage disequilibrium (LD) objects
print.LD.data.frame | Textual and graphical display of linkage disequilibrium (LD) objects
print.locus | Create and Manipulate Locus, Gene, and Marker Objects
print.marker | Create and Manipulate Locus, Gene, and Marker Objects
print.summary.genotype | Allele and Genotype Frequency from a Genotype or Haplotype Object
print.summary.LD.data.frame | Textual and graphical display of linkage disequilibrium (LD) objects

## -- S --

shortsummary.genotype | Undocumented functions
sort.genotype | Order/sort genotype/haplotype object
summary.genotype | Allele and Genotype Frequency from a Genotype or Haplotype Object
summary.LD.data.frame | Textual and graphical display of linkage disequilibrium (LD) objects

## -- W --

write.marker.file | Create genetics data files
write.pedigree.file | Create genetics data files
write.pop.file | Create genetics data files

## -- misc --

%in% | Genotype or Haplotype Objects.
%in%.default | Genotype or Haplotype Objects.
%in%.genotype | Genotype or Haplotype Objects.
%in%.haplotype | Genotype or Haplotype Objects.
==.genotype | Genotype or Haplotype Objects.
==.haplotype | Genotype or Haplotype Objects.
[.genotype | Genotype or Haplotype Objects.
[.haplotype | Genotype or Haplotype Objects.
[<-.genotype | Genotype or Haplotype Objects.
[<-.haplotype | Genotype or Haplotype Objects.