Usage
ki.ibs.joint.dist(x, hyp.1, hyp.2 = "UN", hyp.true = "UN", freqs.ki = get.freqs(x), freqs.true = freqs.ki, markers = intersect(names(freqs.ki), names(freqs.true)), theta.ki = 0, theta.true = theta.ki)
Arguments
x
(optional) An integer matrix specifying a single profile.
hyp.1
A character string giving the hypothesis in the numerator of the $KI$. Should be one of ibdprobs, e.g. "FS" (full sibling) or "PO" (parent/offspring) or "UN" (unrelated). hyp.2
A character string giving the hypothesis in the denominator of the $KI$. Should be one of ibdprobs, e.g. "FS" (full sibling) or "PO" (parent/offspring) or "UN" (unrelated). Defaults to "UN". hyp.true
A character string specifying the true relationship between the case profile and the other profile. Should be one of ibdprobs, e.g. "FS" (full sibling) or "PO" (parent/offspring) or "UN" (unrelated). Defaults to "UN". freqs.ki
A list specifying the allelic frequencies that are used when computing the $KI$.
freqs.true
(optionally) A list specifying the allelic frequencies that are used for computing the probabily distribution of the $KI$ under hyp.true. When not provided, the function will use freqs. One might use different allelic frequencies freqs.rel when for example the case profile and relative come from some population, while $KI$s are computed with frequencies from another population.
markers
Character vector stating the markers for which the KI distribution is derived. Default to the intersection of the markers of freqs.ki and freqs.true.
theta.ki
numeric value specifying the amount of background relatedness.
theta.true
numeric value specifying the amount of background relatedness.