calc_genetic_sim: Calculate genetic similarity among individuals
In simecek/qtl2: Tools for analyzing high-dimensional QTL experiments

Description Usage Arguments Details Value Examples

Calculate genetic similarity among individuals from conditional genotype probabilities.

1 2	calc_genetic_sim(probs, use_grid_only = TRUE, omit_x = TRUE, use_allele_probs = TRUE, quiet = TRUE, n_cores = 1)

`probs`	List of three-dimensional arrays of probabilities, as calculated from `calc_genoprob`.
`use_grid_only`	If `TRUE` and `probs` were calculated with `stepwidth="fixed"`, reduce them to the grid using `probs_to_grid`.
`omit_x`	If `TRUE`, only use the autosomes.
`use_allele_probs`	If `TRUE`, assess similarity with allele probabilities (that is, first run `genoprob_to_alleleprob`); otherwise use the genotype probabilities.
`quiet`	IF `FALSE`, print progress messages.
`n_cores`	Number of CPU cores to use, for parallel calculations. (If `0`, use `detectCores`.)

If use_allele_probs=TRUE (the default), we first convert the genotype probabilities are converted to allele probabilities (using genoprob_to_alleleprob). This is recommended, as then the result is like a empirical kinship coefficient (e.g., the expected value for an intercross is 1/2; using genotype probabilities, the expected value is 3/8).

We then calculate sum_kl (p_ikl p_jkl) where k = position, l = allele, and i,j are two individuals.

For crosses with just two possible genotypes (e.g., backcross), we don't convert to allele probabilities but just use the original genotype probabilities.

A matrix of proportion of matching alleles.

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grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
probs <- calc_genoprob(grav2, step=1, error_prob=0.002)
sim <- calc_genetic_sim(probs)