Man pages for spflanagan/gwscaR
Genome-wide Selection Components Analysis in R
| calc.afs.vcf | Calculate allele frequencies from a vcf file |
| calc.fst.nei | Calculate Fst using Nei's formulation (1-(Hw/2Hb)) |
| calc.fst.wright | Calculate Fst using Wright (1943)'s formulation ((ht-hs)/ht) |
| calc.het | calculate observed heterozygosity |
| calc.mean.fst | Calculate mean pairwise Fsts |
| calc.pi | sliding window pi and rho - across all snps |
| calc.rho | Calculate rho (private alleles) |
| changeorder.df | A function to reorder a data.frame |
| choose.one.snp | Choose one SNP per RAD locus from a vcf |
| combine.vcfs | A function to merge two vcf data frames |
| extract.gt.vcf | A function to pull out only the genotype fields from... |
| fst.ibd.byloc | Calculate isolation by distance per locus |
| fst.one.plink | Calculate pairwise fsts from a dataset in ped format |
| fst.one.vcf | Calculate fsts from a single vcf |
| fst.plot | Plot genome-wide statistics from a data frame. |
| fst.plot.rect | Plot genome-wide statistics from a data frame with... |
| fst.pst.byloc | Compare Pst and Fst locus by locus from a ped file |
| fst.sig | Find significant loci using chi-square test |
| fst.two.vcf | Calculate pairwise fst between two separate vcf files |
| get.nj | Generate a distance matrix for a SNP using fsts |
| gwsca | Conduct selection components analysis |
| gwsca.vioplot | Create violin plots with |
| infer.mat.alleles | A function to infer maternal alleles from a vcf file |
| outer.legend | Add a legend to the margins of a multiplot figure |
| pairwise.fst | Calculate pairwise Fst values |
| pairwise.pst | Calculate pairwise Pst between population pairs |
| parse.vcf | Read in a vcf file |
| pcadapt_subset | Subset a ped file and run pcadapt on it |
| plotting.structure | This plots the output of structure |
| popgen.sim | Simulate genetic data for populations with different allele... |
| pst.mantel | Calulate pairwise Psts and test for IBD |
| sem | Calculate the standard error of the mean |
| sliding.avg | Calculate a sliding average |
| sliding.window | Calculate a sliding window |
| std.by.mean | Standardize a variable by its mean |
| treemix.cov.plot | Plot covariance matrix from treemix |
| treemix.from.vcf | Generate a treemix file from vcf |
| vcf2coanAF | Convert a vcf df to a coancestry input file |
| vcf2coanGT | Convert a vcf df to a coancestry input file |
| vcf2dadiSNPs | Convert a vcf file to a SNPs input file for dadi |
| vcf2gpop | Convert a vcf df to a genepop file |
| vcf.alleles | Extract alleles from a vcf row |
| vcf.cov.ind | Calculate per-individual coverage from a vcf file |
| vcf.cov.loc | Calculate per-locus coverage from a vcf file |
