# mungeData: mungeData In HWxtest: Exact Tests for Hardy-Weinberg Proportions

## Description

Utility functions for handling genotype counts and arranging data

remove missing alleles

converts matrix to vector

Clears upper-right of matrix

## Usage

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13``` ```fillUpper(gmat) alleleCounts(gmat) vec.to.matrix(gvec, alleleNames = "") remove.missing.alleles(gmat) matrix.to.vec(gmat) clearUpper(gmat) df.to.matrices(df, sep = "/") ```

## Arguments

 `gmat` a matrix of non-negative integers representing genotype counts. In a matrix of genotype counts, `a[i,j]` and `a[j,i]` both represent the same heterozygote. Only the lower-left half of `gmat` is used. Numbers along the diagonal represent counts of the homozygotes. `gvec` vector containing `k(k+1)/2` genotype counts. All non-negative integers. Genotype counts should be in the order: `a11, a21, a22, a31, a32, ..., akk` `alleleNames` an optional list of names for the alleles. The length should be k `df` a dataframe containing individual genotypes. Each row represents an individual. The first column, named “pop” names the population. Each other column is named for a particular locus. The genotypes are as “123/124” `sep` For a dataframe, this is the separator character. typically “/”

## Details

Interconvert between different formats for genotype counts.

Let `k` be the number of alleles:

• `clearUpper` fills the upper-right half of the k x k matrix with `NA`

• `fillUpper` makes the k x k matrix symmetrical by filling the upper-right half with numbers from the lower half.

• `vec.to.matrix` converts genotype counts in vector form and returns a matrix. The vector must have k(k+1)/2 non-negative integers.

• `matrix.to.vec` converts a k x k matrix of genotype counts to a vector of length k(k+1)/2

• `alleleCounts` returns a vector of length k containing the numbers of each allele. The sum of this vector will be twice the number of diploids in the sample.

• `remove.missing.alleles` returns a matrix with no `0`'s for allele counts

• `df.to.matrices` converts a data frame to a list of genotype count matrices. The data frame should be of the kind produced in the package `adegenet` with `genind2df`

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## Examples

 ```1 2 3``` ```gvec <- c(0,3,1,5,18,1,3,7,5,2) gmat <- vec.to.matrix(gvec, alleleNames=letters[1:4]) alleleCounts(gmat) ```

HWxtest documentation built on May 31, 2019, 9:04 a.m.