This vignette will introduce you to how the basic genetic parameters like the allele frequency, the genotype frequency and Hardy-Weinberg Equilibrium results are calculated with `mixIndependR`

.

## Data Import

The dataset imported should be in a format of the genotype data with individuals in rows and markers in columns. Excel, csv and vcf file format are compatible.

`mixexample`

is an attached data in this package, which is the genotypes of 2504 individuals on 100 unlined variants including 6 STRs and 94 SNPs.

## Basic Genetic Parameters

`AlleleFreq`

calculates the allele frequencies for one dataset.

`p <- AlleleFreq(x,sep = "\\|")`

`GenotypeFreq`

calculates the observed or expected genotype frequency. If `expect=FALSE`

, the observed genotype frequencies from the original dataset will be calculated. If `expected=TRUE`

, the expected genotype probabilities from allele frequency table under Hardy-Weinberg Equilibrium will be exported.

```
G <- GenotypeFreq(x,sep = "\\|",expect = FALSE)
G0 <- GenotypeFreq(x,sep = "\\|",expect = TRUE)
```

`Heterozygous`

test the heterozygosity of each individuals at each locus and output a table with `0`

denoting homozygous and `1`

heterozygous.

`h <-Heterozygous(x,sep = "\\|") ####or Just use Heterozygous(x)`

`RxpHetero`

calculate Real or Expected Average Heterozygosity at each locus. If `HWE=TRUE`

, this function will calculate the expected heterozygosities under Hardy-Weinberg Equilibrium; If `HWE=FALSE`

, this function will calculate the real average heterozygosities.

`H <- RxpHetero(h,p,HWE=TRUE)`

`AlleleShare`

calculates the table of number of shared alleles for each pair of individuals at each locus.If `replacement=TRUE`

, the pairs are formed with replacement; if `replacement=FALSE`

, the pairs are formed without replacement. When the sample size is large, `replacement=F`

is much faster.

`AS<-AlleleShare(x,sep = "\\|",replacement = FALSE) `

`RealProAlleleShare`

and `ExpProAllelShare`

calculate the average proportions and the expected probabilities of sharing 0,1 and 2 alleles at each locus.

```
e <-RealProAlleleShare(AS)
e0<-ExpProAlleleShare(p)
```

`HWE_Chisq`

test the Hardy-Weinberg Equilibrium with Pearsonâ€™s Chi-square test. `B`

is an integer specifying the number of replicates used in the Monte Carlo test.

```
HWE_pvalue <-HWE.Chisq(G,G0,rescale.p = T,simulate.p.value = T,B=2000)
```