calc.mean.fst: Calculate mean pairwise Fsts
In spflanagan/gwscaR: Genome-wide Selection Components Analysis in R
Description
Usage
Arguments
Value
Description
Calculate mean pairwise Fsts
Usage
1
2
calc.mean.fst(vcf, pop.list1, pop.list2, maf.cutoff = 0.05,
cov.thresh = 0.2, locus.info = NULL)
Arguments
vcf
A data.frame containing the contents of a vcf file
pop.list1
A list of populations. This will be used to subset the vcf file to extract individuals for each pairwise comparison so it must contain a string found in individual IDs.
pop.list2
A list of populations. Same requirements as pop.list1. Individuals from populations in pop.list1 will be compared to individuals in pop.list2.
maf.cutoff
An optional value for the minimum allele frequency. Must be between 0 and 1 (default is 0.05)
cov.thresh
Coverage threshold between 0 and 1 (default is 0.2)
locus.info
A vector of column names that contain the information for the vcf loci (by default, if not specified, is the first 9 columns of vcf)
Value
mu A data.frame containing the columns: Chrom, Pos, SNP, Sum.Fst, Count, and Mean.Fst. Sum.Fst is the total sum of Fst values, which are divided by Count (the number of comparisons the locus was present in) to generate Mean.Fst.
spflanagan/gwscaR documentation built on Nov. 14, 2019, 9:16 p.m.
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Description Usage Arguments Value
Description
Calculate mean pairwise Fsts
Usage
1 2 | calc.mean.fst(vcf, pop.list1, pop.list2, maf.cutoff = 0.05,
cov.thresh = 0.2, locus.info = NULL)
|
Arguments
vcf |
A data.frame containing the contents of a vcf file |
pop.list1 |
A list of populations. This will be used to subset the vcf file to extract individuals for each pairwise comparison so it must contain a string found in individual IDs. |
pop.list2 |
A list of populations. Same requirements as pop.list1. Individuals from populations in pop.list1 will be compared to individuals in pop.list2. |
maf.cutoff |
An optional value for the minimum allele frequency. Must be between 0 and 1 (default is 0.05) |
cov.thresh |
Coverage threshold between 0 and 1 (default is 0.2) |
locus.info |
A vector of column names that contain the information for the vcf loci (by default, if not specified, is the first 9 columns of vcf) |
Value
mu A data.frame containing the columns: Chrom, Pos, SNP, Sum.Fst, Count, and Mean.Fst. Sum.Fst is the total sum of Fst values, which are divided by Count (the number of comparisons the locus was present in) to generate Mean.Fst.
R Package Documentation
Browse R Packages
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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