calc_tajimas_d: Tajima's D from SNP data.

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

Tajima's D from SNP data.

Description

Tajimas_D calculates Tajima's theta/pi, Watterson's theta, and Tajima's D over a sliding window.

Usage

calc_tajimas_d(
  x,
  facets = NULL,
  sigma = NULL,
  step = 2 * sigma,
  par = FALSE,
  triple_sigma = TRUE,
  global = FALSE,
  verbose = FALSE
)

Arguments

x	snpRdata. Input SNP data.
facets	character. Categorical metadata variables by which to break up analysis. See Facets_in_snpR for more details. If no snp level facets are provided, the calculated Tajima's D will be for the entire genome.
sigma	numeric, default NULL. Sliding window size, in kilobases. Each window will include all SNPs within 3*sigma or sigma kilobases depending on the triple_sigma argument. If either sigma or step are NULL, the entire snp subfacet will be done at once (for example, the whole chromosome).
step	numeric or NULL, default 2*sigma (non-overlapping windows). Number of bases to move between each window, in kilobases. If either sigma or step are NULL, the entire snp subfacet will be done at once (for example, the whole chromosome).
par	numeric or FALSE, default FALSE. If numeric, the number of cores to use for parallel processing.
triple_sigma	logical, default TRUE. If TRUE, sigma will be tripled to create windows of 6*sigma total.
global	logical, default FALSE. If TRUE, all window parameters will be ignored and the global Tajima's D across all sites will instead be calculated. In this instance, global_x values will be merged into the weighted.means slot instead of weighted mean values and no values will be merged into the window.stats slot.
verbose	logical, default FALSE. If TRUE progress will be printed to the console.

Details

Tajima's D compares estimates of theta based on either the number of observed pairwise differences (Tajima's theta) and the number of substitutions vs expected total tree length (Watterson's Theta). Since low frequency minor variants contribute to these statistics and they rely on the ratio of the number of variants vs the number of sequenced non-polymorphic sites, this function should only be run on data that is unfiltered aside from the removal of poorly sequenced bases, etc.

The data can be broken up categorically by either SNP and/or sample metadata, as described in Facets_in_snpR.

Value

snpRdata object, with Watterson's Theta, Tajima's Theta, and Tajima's D for each window merged in to the window.stats slot.

Author(s)

William Hemstrom

References

Tajima, F. (1989). Genetics

Examples

# slow, so not run
## Not run: 
# broken by population, windows across linkage group
x <- calc_tajimas_d(stickSNPs, facets = "chr.pop", sigma = 200, step = 50)
get.snpR.stats(x, "chr.pop", "tajimas_d")

# the entire population at once, note that sigma and step are NULL and
# no chromosome/linkage group/scaffold/etc set.
# this will calculate overall tajima's D without a window for each population.
x <- calc_tajimas_d(stickSNPs, facets = "pop")
get.snpR.stats(x, "pop", "tajimas_d")

# for the overall dataset, note that sigma and step are NULL
# this will calculate overall tajima's D for each chr/pop
x <- calc_tajimas_d(stickSNPs, facets = "chr.pop")
get.snpR.stats(x, "pop.chr", "tajimas_d")

## End(Not run)

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