Man pages for spflanagan/gwscaR
Genome-wide Selection Components Analysis in R

calc.afs.vcfCalculate allele frequencies from a vcf file
calc.fst.neiCalculate Fst using Nei's formulation (1-(Hw/2Hb))
calc.fst.wrightCalculate Fst using Wright (1943)'s formulation ((ht-hs)/ht)
changeorder.dfA function to reorder a data.frame one SNP per RAD locus from a vcf
combine.vcfsA function to merge two vcf data frames function to pull out only the genotype fields from...
fst.ibd.bylocCalculate isolation by distance per locus pairwise fsts from a dataset in ped format fsts from a single vcf
fst.plotPlot genome-wide statistics from a data frame.
fst.plot.rectPlot genome-wide statistics from a data frame with...
fst.pst.bylocCompare Pst and Fst locus by locus from a ped file
fst.sigFind significant loci using chi-square test
fst.two.vcfCalculate pairwise fst between two separate vcf files
gwscaConduct selection components analysis
infer.mat.allelesA function to infer maternal alleles from a vcf file
pairwise.fstCalculate pairwise Fst values
pairwise.pstCalculate pairwise Pst between population pairs
parse.vcfRead in a vcf file
plotting.structureThis plots the output of structure
pst.mantelCalulate pairwise Psts and test for IBD
semCalculate the standard error of the mean
vcf.allelesExtract alleles from a vcf row
vcf.cov.indCalculate per-individual coverage from a vcf file
vcf.cov.locCalculate per-locus coverage from a vcf file
spflanagan/gwscaR documentation built on April 30, 2018, 2:30 a.m.