calc_smoothed_averages: Gaussian smooth or average statistics across sliding windows.

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

Gaussian smooth or average statistics across sliding windows.

Description

Calculates optionally gaussian smoothed average values for statistics and the genomic position at which it was observed, splitting by any requested variables.

Usage

calc_smoothed_averages(
  x,
  facets = NULL,
  sigma,
  step = 2 * sigma,
  nk = TRUE,
  stats.type = c("single", "pairwise"),
  par = FALSE,
  triple_sigma = FALSE,
  gaussian = TRUE,
  verbose = FALSE
)

Arguments

x	snpRdata object.
facets	character or NULL, default NULL. Categories by which to break up windows.
sigma	numeric. Designates the width of windows in kilobases. Full window size is 6*sigma or sigma kilobases depending on the triple_sigma argument.
step	numeric or NULL, default default 2*sigma (non-overlapping windows). Designates the number of kilobases between each window centroid. If NULL, windows are centered on each SNP.
nk	logical, default TRUE. If TRUE, weights SNP contribution to window averages by the number of observations at those SNPs.
stats.type	character, default c("single", "pairwise"). Designates the statistic(s) to smooth, either "single", "pairwise", or c("single", "pairwise"). See details.
par	numeric or FALSE, default FALSE. If numeric, the number of cores to use for parallel processing.
triple_sigma	Logical, default FALSE If TRUE, sigma will be tripled to create windows of 6*sigma total.
gaussian	Logical, default TRUE. If TRUE, windows will be gaussian smoothed. If not, windows will be raw averages.
verbose	Logical, default FALSE. If TRUE, some progress updates will be printed to the console.

Details

Averages for multiple statistics can be calculated at once. If the statistics argument is set to c("pairwise", "single"), all calculated stats will be run. If it is set to "single", then all non-pairwise statistics (pi, ho, maf, etc.) will be bootstrapped, if it is set to "pairwise", then all pairwise statistics (fst) will be bootstrapped. Individual statistics currently cannot be requested by name, since the computational differences to add additional types is minimal.

The data can be broken up categorically by snp or sample metadata, as described in Facets_in_snpR. Windows will only be calculated using only SNPs on the same level of any provided facets. NULL and "all" facets work as normally described in Facets_in_snpR.

As described in Hohelohe et al. (2010), the contribution of individual SNPs to window averages can be weighted by the number of observations per SNP by setting the nk argument to TRUE, as is the default. For bootstraps, nk values are randomly drawn for each SNP in each window. SNPs can also optionally be weighted by their proximity to the window centroid using a gaussian kernal.

Centers for windows can either every SNP (if no step size is provided), or every step kilobases from the 0 position of each snp level facet category (chromosome, etc.).

The size of sliding windows are defined by the "sigma" argument. Note that this value, as well as that provided to the "step" argument, are given in kilobases. Each window will include SNPs within 3*sigma kilobases from the window center (if the triple_sigma option is selected). Past this point, the effect of each additional SNP on the window average would be very small, and so they are dropped for computational efficiency (see Hohenlohe (2010)).

Value

snpRdata object with smoothed averages for any requested statistics merged into the window.stats or pairwise.window.stats slots.

Author(s)

William Hemstrom

References

Hohenlohe et al. (2010). PLOS Genetics

Examples

## Not run: 
# add a few statistics
x <- calc_pi(stickSNPs, "chr.pop")
x <- calc_ho(x, "chr.pop")
x <- calc_pairwise_fst(x, "chr.pop")
# smooth with a fixed slide between window centers.
x <- calc_smoothed_averages(x, "chr.pop", sigma = 200, step = 50)
get.snpR.stats(x, "chr.pop", "single.window") # pi, ho
get.snpR.stats(x, "chr.pop", "pairwise.window") # fst

## End(Not run)

hemstrow/snpR documentation built on Dec. 13, 2024, 4:27 a.m.