calc_directionality: Calculate the directionality index from a 2d site frequency...

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

Calculate the directionality index from a 2d site frequency spectrum.

Description

Calculates the directionality index based on a 2d SFS according to Peter and Slatkin (2013). Input spectra can be created using the calc_sfs function, using a provided snpRdata object, or passed from other programs. Spectra must be not be folded.

Usage

calc_directionality(
  x,
  facet = NULL,
  pops = NULL,
  projection = NULL,
  update_bib = FALSE
)

Arguments

x	snpRdata object or matrix, default NULL. A snpRdata from which to calculate a SFS. Alternatively, a 2d site frequency spectra stored in a matrix, with an additional "pop" or "pops" attribute containing population IDs, such as c("POP1", "POP2"), where the first pop corresponds to matrix columns and the second to matrix rows. These objects can be produced from a dadi input file using make_SFS. Note that if x is a snpRdata object, snp metadata columns named "ref" and "anc" containing the identity of the derived and ancestral alleles, respectively, must be present.
facet	character, default NULL. Passed to calc_sfs – see documentation there for details. Ignored if a sfs is provided.
pops	character, default NULL. Passed to calc_sfs – see documentation there for details. Ignored if a sfs is provided.
projection	numeric, default NULL. Passed to calc_sfs – see documentation there for details. Ignored if a sfs is provided.
update_bib	character or FALSE, default FALSE. If a file path to an existing .bib library or to a valid path for a new one, will update or create a .bib file including any new citations for methods used. Useful given that this function does not return a snpRdata object, so a citations cannot be used to fetch references.

Details

Essentially, the directionality index measures the difference in derived allele frequency between two populations to determine the directionality of population spread between the two. Since the "destination" population is sourced from but experienced more genetic drift than the "source" population, it should have relatively more high-frequency derived alleles after the removal of fixed ancestral alleles. See Peter and Slatkin (2013) for details.

Value

A numeric value giving the directionality with a "direction" attribute designating the direction between the two populations.

References

Peter, B. M., & Slatkin, M. (2013). Detecting range expansions from genetic data. Evolution, 67(11), 3274-3289.

Examples

## Not run: 
# directionality can be calculated without first calculating a SFS
calc_directionality(stickSNPs, facet ="pop", pops = c("ASP", "PAL"), projection = c(10, 10))

# an existing SFS can also be fed in. This may be handy if you get a SFS from elsewhere.
sfs <- calc_sfs(stickSNPs, "pop", c("ASP", "PAL"), c(10, 10), fold = FALSE)
calc_directionality(sfs)

## End(Not run)

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