calc_prop_poly: Calculate the proportion of polymorphic loci.

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Calculate the proportion of polymorphic loci.

Description

Calculates the proportion of polymorphic (genotyped) loci for any combination of SNP and sample facets. Note: per window counts of polymorphic loci can be calculated using calc_tajimas_d.

Usage

calc_prop_poly(x, facets = NULL)

Arguments

x	snpRdata object
facets	facets over which to check for polymorphic loci. Can be any combination of SNP/sample facets. See Facets_in_snpR for details.

Details

Note that per window counts of polymorphic loci can be calculated using calc_tajimas_d (contained in the num_seg column). Dividing this by the n_snps column will return the proportion of polymorphic loci in each window if that is desired!

Value

A snpRdata object with prop_poly merged into the weighted.means slot.

Author(s)

William Hemstrom

Examples

# base facet
x <- calc_prop_poly(stickSNPs)
get.snpR.stats(x, stats = "prop_poly")$weighted.means

# multiple facets
x <- calc_prop_poly(stickSNPs, c("pop", "fam", "pop.fam", 
                                 "pop.fam.chr", "chr"))
get.snpR.stats(x, c("pop", "fam", "pop.fam", "pop.fam.chr", "chr"), 
               stats = "prop_poly")$weighted.means

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.