calcHet: Calculate individual heterozygosity
In gbradburd/popgenstuff: Handy Functions for PopGen Analysis in R
Description
Usage
Arguments
Details
Value
Description
Calculate individual heterozygosity
Usage
1
Arguments
gt
A genotype matrix with N rows and
L columns, where N is the number
of individuals and L is the number of
loci, for which the i,jth element
gives the number of the counted allele in each
individual at each locus.
nLoci
An optional argument giving the number of genotyped
base pairs in each individual. If not specified,
this is assumed to be the number of non-missing
genotypes in each row of gt. Default is
NULL.
Details
The data matrix gt should consist of
0s, 1s, and 2s, with missing data indicated with
NA. This can be generated from a VCF file
using vcf2R. If nLoci is not
specified, and gt consists only of
polymorphic loci, this function will return
heterozygosity at polymorphic sites, which may not
be comparable across datasets.
Value
A vector giving the proportion of loci that are
heterozygous in each individual.
gbradburd/popgenstuff documentation built on Oct. 16, 2021, 12:05 a.m.
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Description Usage Arguments Details Value
Description
Calculate individual heterozygosity
Usage
1 |
Arguments
gt |
A genotype matrix with N rows and L columns, where N is the number of individuals and L is the number of loci, for which the i,jth element gives the number of the counted allele in each individual at each locus. |
nLoci |
An optional argument giving the number of genotyped
base pairs in each individual. If not specified,
this is assumed to be the number of non-missing
genotypes in each row of |
Details
The data matrix gt should consist of
0s, 1s, and 2s, with missing data indicated with
NA. This can be generated from a VCF file
using vcf2R. If nLoci is not
specified, and gt consists only of
polymorphic loci, this function will return
heterozygosity at polymorphic sites, which may not
be comparable across datasets.
Value
A vector giving the proportion of loci that are heterozygous in each individual.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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