fst.one.vcf: Calculate fsts from a single vcf
In spflanagan/gwscaR: Genome-wide Selection Components Analysis in R
Description
Usage
Arguments
Value
Description
Calculate fsts from a single vcf
Usage
1
fst.one.vcf(vcf.row, group1, group2, cov.thresh = 0.2, maf = 0.05)
Arguments
vcf.row
A row of a data.frame in vcf format
group1
A list of individual names for pop1
group2
A list of individual names for pop2
cov.thresh
A proportion of individuals required for genotyping individuals (default is 0.2)
maf
A minimum allele frequency (default is 0.05)
Value
out A data.frame with columns:
Hs1 (expected heterozygosity in pop 1), Hs2 (expected heterozygosity in pop2),
Hs (expected heterozygosity within pops), Ht (expected heterozygosity between pops),
Fst, NumAlleles, Num1 (number of individuals in pop1), and Num2 (number of individuals in pop2)
spflanagan/gwscaR documentation built on Nov. 14, 2019, 9:16 p.m.
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Description Usage Arguments Value
Description
Calculate fsts from a single vcf
Usage
1 | fst.one.vcf(vcf.row, group1, group2, cov.thresh = 0.2, maf = 0.05)
|
Arguments
vcf.row |
A row of a data.frame in vcf format |
group1 |
A list of individual names for pop1 |
group2 |
A list of individual names for pop2 |
cov.thresh |
A proportion of individuals required for genotyping individuals (default is 0.2) |
maf |
A minimum allele frequency (default is 0.05) |
Value
out A data.frame with columns: Hs1 (expected heterozygosity in pop 1), Hs2 (expected heterozygosity in pop2), Hs (expected heterozygosity within pops), Ht (expected heterozygosity between pops), Fst, NumAlleles, Num1 (number of individuals in pop1), and Num2 (number of individuals in pop2)
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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