get.snpR.stats: Pull calculated statistics from snpRdata objects.

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

Pull calculated statistics from snpRdata objects.

Description

A convenience function that pulls statistics of any specified type at particular facets from a snpRdata object.

Usage

get.snpR.stats(x, facets = NULL, stats = "single", bootstraps = FALSE)

Arguments

x	snpRdata object.
facets	character or NULL, default NULL. Facets for which to fetch data.
stats	character or NULL, default NULL. Statistics for which to fetch data. Named identically as in the function used to calculate them (such as calc_pi). See description for list. Alternatively, a type of statistic can be requested–see description for details.
bootstraps	logical, default FALSE. If FALSE, bootstraps will not be returned even if they have been created for the requested statistics. Since bootstrapped datasets are often quite large, returning these may use a lot of additional memory.

Details

Facets are specified as described in Facets_in_snpR. If facets = "all", data for all facets, including the base facet, will be returned. By default, the base facet alone will be returned.

Different statistics are returned either by named statistic or by type.

Types

• single: non-pairwise, non-window statistics (pi, ho, etc.)

• pairwise: pairwise, non-window statistics (Fst).

• single.window: non-pairwise, sliding window statistics.

• pairwise.window: pairwise, sliding window statistics.

• LD: linkage disequilibrium matrices and tables.

• bootstraps: bootstraps of window statistics.

• genetic_distance: genetic distances

• allele_frequency_matrix: allele frequency matrices.

• geo_dist: geographic distances.

• ibd: isolation by distance results.

• sample: sample stats.

• pop: population summary statistics.

• weighted.means: Weighted means of SNP statistics per facet level.

Statistics

• ho: Observed heterozygosity, via calc_ho.

• pi: pi (expected number of pairwise differences, via calc_pi).

• maf: minor allele frequencies (and major/minor counts and identities), via calc_maf.

• private: private allele identities, via calc_private.

• association: results from phenotypic association tests, via calc_association.

• hwe: Hardy-Weinberg Equilibrium p-values, via calc_hwe.

• tajimas_d: Tajima's D, Watterson's Theta, and Tajima's Theta, via calc_tajimas_d.

• fst: Pairwise Fst, via calc_pairwise_fst.

• het_hom_ratio: Heterozygote/Homozygote ratios within individuals, via calc_het_hom_ratio.

• ne: Effective population size estimates, via calc_ne.

• ld: Pairwise linkage disequilibrium, via calc_pairwise_ld.

• genetic_distances: Genetic distances, calc_genetic_distances.

• isolation_by_distance: Genetic isolation by distance metrics, via calc_isolation_by_distance.

• geographic_distance: Geographic distances between samples–does not use genetic data. Calculated during calc_isolation_by_distance, but fetchable independently here.

• random_forest Random forest snp-specific responses, see run_random_forest.

Author(s)

William Hemstrom

Examples

# generate some statistics
dat <- calc_pi(stickSNPs, "pop")
dat <- calc_pairwise_fst(dat, "pop")

# fetch pi
get.snpR.stats(dat, "pop", "pi")
# fetch fst
get.snpR.stats(dat, "pop", "fst")
# fetch both
get.snpR.stats(dat, "pop", c("pi", "fst"))

# return a type of statistic instead of specific statistics
dat <- calc_ho(stickSNPs, "chr.pop")
get.snpR.stats(dat, "chr.pop", "weighted.means")

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