Description Usage Arguments Details Examples
Utility functions for handling genotype counts and arranging data
remove missing alleles
converts matrix to vector
Clears upperright of matrix
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 = "/")

gmat 
a matrix of nonnegative integers representing genotype counts. In a matrix of genotype counts, 
gvec 
vector containing 
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 “/” 
Interconvert between different formats for genotype counts.
Let k
be the number of alleles:
clearUpper
fills the upperright half of the k x k matrix with NA
fillUpper
makes the k x k matrix symmetrical by filling the upperright 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 nonnegative 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
none
none
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)

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