calc_ne: Calculate effective population size.

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

Calculate effective population size.

Description

Calculates effective population size for any given sample-level facets via interface with the NeEstimator v2 program by Do et al. (2013).

Usage

calc_ne(
  x,
  facets = NULL,
  chr = NULL,
  NeEstimator_path = "/usr/bin/Ne2-1.exe",
  mating = "random",
  pcrit = c(0.05, 0.02, 0.01),
  methods = "LD",
  temporal_methods = c("Pollak", "Nei", "Jorde"),
  temporal_details = NULL,
  max_ind_per_pop = NULL,
  nsnps = nrow(x),
  outfile = "ne_out",
  verbose = TRUE,
  cleanup = TRUE
)

Arguments

x	snpRdata object. The data for which Ne will be calculated.
facets	character, default NULL. Categorical metadata variables by which to break up analysis. See Facets_in_snpR for more details. Only sample specific categories are allowed, all others will be removed. If NULL, Ne will be calculated for all samples. Note that for the temporal method specifically, and unusually for snpR, components of complex facets need to be provided alphabetically ("fam.pop" not "pop.fam").
chr	character, default NULL. An optional but recommended SNP specific categorical metadata variable which designates chromosomes/linkage groups/etc. Pairwise LD scores for SNPs with the same level of this variable will be not be used to calculate Ne. Since physical linkage can bias Ne estimates, providing a value here is recommended.
NeEstimator_path	character, default "/usr/bin/Ne2-1.exe". Path to the NeEstimator executable.
mating	character, default "random". The mating system to use. Options: "random" Random mating. "monogamy" Monogamous mating.
pcrit	numeric, default c(.05, .02, .01). Minimum minor allele frequencies for which to calculate Ne. Rare alleles can bias estimates, so a range of values should be checked.
methods	character, default "LD". LD estimation methods to use. Options: "LD" Linkage Disequilibrium based estimation. "het" Heterozygote excess. "coan" Coancestry based. "temporal" Temporal-based. Requires muliple time-points for a population
temporal_methods	character, default c("Pollak", "Nei", "Jorde"). Temporal methods to use. See NeEstimator documentation.
temporal_details	Three or four column data.frame or NULL, default NULL. Details for the generation/population layout to use for the temporal method if requested. Columns one and two are levels of the provided facet given corresponding to the first and second time point of the population, respectively. Column three is a number indicating the number of generations between samples. Column four is optionally the census population size at time one. Any values other than zero will use NeEstimator's Plan II. Note that level components of complex facets need to be provided in the same order as the facet (for "fam.pop", family "A" population "ASP" should be provided as "A.ASP"), as usual.
max_ind_per_pop	numeric, default NULL. Maximum number of individuals to consider per population.
nsnps	numeric, default nrow(x). The number of SNPs to use for the analysis, defaulting to all of the snps in the data set. Using very large numbers of SNPs (10k+) doesn't usually improve the ne estimates much but costs a lot of time, since computing time scales with the square of the number of sites.
outfile	character, default "ne_out". Prefix for output files. Note that this function will return outputs, so there isn't a strong reason to check this. At the moment, this cannot be a full file path, just a file prefix ('test_ne' is OK, '~/tests/test_ne' is not).
verbose	Logical, default FALSE. If TRUE, some progress updates will be reported.
cleanup	logical, default TRUE. If TRUE, the NeEstimator output directory will be removed following processing.

Details

Since physical linkage can cause miss-estimation of Ne, an optional snp-level facet can be provided which designates chromosomes or linkage groups. Only pairwise LD values between SNPs on different facet levels will be used.

Ne can be calculated via three different methods:

• "LD" Linkage Disequilibrium based estimation.

• "Het" Heterozygote excess.

• "Coan" Coancestry based.

For details, please see the documentation for NeEstimator v2.

Value

A named list containing estimated Ne values (named "ne") and the original provided data, possibly with additional LD values (named "x").

Author(s)

William Hemstrom

References

Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR. 2014 NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol. Ecol. Resour. 14, 209–214. (doi:10.1111/1755-0998.12157)

Examples

## Not run: 
# not run, since the path to NeEstimator may vary
# calculate Ne, noting not to use LD between SNPs on the 
# same chromosome equivalent ("chr") for every population.
ne <- calc_ne(stickSNPs, facets = "pop", chr = "chr")
get.snpR.stats(ne, "pop", stat = "ne")
## End(Not run)

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