inbreedR (version 0.3.0)

r2_hf: Expected r2 between standardized multilocus heterozygosity (h) and inbreeding level (f)

Description

Expected r2 between standardized multilocus heterozygosity (h) and inbreeding level (f)

Usage

r2_hf(genotypes, type = c("msats", "snps"), nboot = NULL,
  parallel = FALSE, ncores = NULL, CI = 0.95, subsets = NULL,
  nboot_loci = 100)

Arguments

genotypes

data.frame with individuals in rows and loci in columns, containing genotypes coded as 0 (homozygote), 1 (heterozygote) and NA (missing)

type

specifies g2 formula to take. Type "snps" for large datasets and "msats" for smaller datasets.

nboot

number of bootstraps over individuals to estimate a confidence interval around r2(h, f)

parallel

Default is FALSE. If TRUE, bootstrapping and permutation tests are parallelized

ncores

Specify number of cores to use for parallelization. By default, all available cores but one are used.

CI

confidence interval (default to 0.95)

subsets

deprecated. a vector specifying the sizes of marker-subsets to draw. For a subset of 20 markers, subsets = c(2, 5, 10, 15, 20) could be a reasonable choice. The minimum subset size is 2 and the maximum is the number of markers in the data.

nboot_loci

deprecated. number of re-draws per subset of loci.

Value

• call
  function call.
• r2_hf_full
  expected r2 between inbreeding and sMLH for the full dataset
• r2_hf_boot
  expected r2 values from bootstrapping over individuals
• CI_boot
  confidence interval around the expected r2
• r2_hf_res
  expected r2 for each randomly subsetted dataset
• summary_r2_hf_res
  r2 mean and sd for each number of subsetted loci
• nobs
  number of observations
• nloc
  number of markers

References

Slate, J., David, P., Dodds, K. G., Veenvliet, B. A., Glass, B. C., Broad, T. E., & McEwan, J. C. (2004). Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data. Heredity, 93(3), 255-265.

Szulkin, M., Bierne, N., & David, P. (2010). HETEROZYGOSITY-FITNESS CORRELATIONS: A TIME FOR REAPPRAISAL. Evolution, 64(5), 1202-1217.

Examples

data(mouse_msats)
genotypes <- convert_raw(mouse_msats)
(out <- r2_hf(genotypes, nboot = 100, type = "msats", parallel = FALSE, 
              subsets = c(2,4,6,8,10,12), nboot_loci = 100))
plot(out)