Population Genetics

Documentation for package ‘genetics’ version 1.3.8.1.3

Help Pages

-- 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 --

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 --

-- 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.