calc_isolation_by_distance: Calculate Isolation by Distance

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

Calculate Isolation by Distance

Description

Calculates Isolation by Distance (IBD) for snpRdata objects by comparing the genetic distance between samples or sets of samples to the geographic distances between samples or sets of samples. IBD calculated via a mantel test.

Usage

calc_isolation_by_distance(
  x,
  facets = NULL,
  x_y = c("x", "y"),
  genetic_distance_method = "Edwards",
  interpolate = "bernoulli",
  ...
)

Arguments

x	snpRdata object
facets	character, default NULL. Facets over which to calculate IBD, as described in Facets_in_snpR.
x_y	character, default c("x", "y"). Names of the columns containing geographic coordinates where samples were collected. There is no need to specify projection formats. The first should be longitude, the second should be latitude.
genetic_distance_method	character, default "Edwards". The genetic distance method to use, see calc_genetic_distances.
interpolate	Character or FALSE, default "bernoulli". If transforming to "sn" format, notes the interpolation method to be used to fill missing data. Options are "bernoulli", "af", "iPCA", or FALSE. See format_snps for details.
...	Additional arguments passed to mantel.randtest

Details

Genetic distance is calculated via calc_genetic_distances. Geographic distances are taken as-is for individual-individual comparisons and by finding the geographic mean of a group of samples when sample level facets are requested using the methods described by geomean. Note that this means that if many samples were collected from the same location, and those samples compose a single level of a facet, the mean sampling location will be that single location.

IBD is calculated by comparing geographic and genetic distances using a mantel test via mantel.randtest.

Note that geographic distance objects are also included in the returned values.

Value

A snpRdata object with both geographic distance and IBD results merged into existing data.

Author(s)

William Hemstrom

See Also

mantel.randtest, calc_genetic_distances

Examples

# calculate ibd for several different facets
## Not run: 
y <- stickSNPs
sample.meta(y) <- cbind(sample.meta(y), x = rnorm(ncol(y)), y = rnorm(ncol(y)))
y <-calc_isolation_by_distance(y, facets = c(".base", "pop", "pop.chr","pop.chr.fam"))
res <- get.snpR.stats(y, "pop.chr", "ibd") # fetch results
res
plot(res$chr.pop$groupV$Edwards) # plot perms vs observed

## End(Not run)

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