zeroIBD {ibdsim2} | R Documentation |
Probability of zero IBD
Description
Estimate the probability of no IBD sharing in a pairwise relationship.
Usage
zeroIBD(sims, ids = NULL, threshold = 0, unit = "cm")
Arguments
sims |
A list of genome simulations, as output by |
ids |
A vector with two ID labels. If NULL (default), these are deduced
from the |
threshold |
A nonnegative number (default:0). Only IBD segments longer than this are included in the computation. |
unit |
The unit of measurement for |
Value
A list with the following two entries:
-
zeroprob
: The fraction ofsims
in whichids
have no IBD sharing -
stErr
: The standard error ofzeroprob
Examples
###
# The following example computes the probability of
# no IBD sharing between a pair of fourth cousins.
# We also show how the probability is affected by
# truncation, i.e., ignoring short segments.
###
# Define the pedigree
x = cousinPed(4)
cous = leaves(x)
# Simulate (increase N!)
s = ibdsim(x, N = 10)
# Probability of zero ibd segments. (By default all segs are used)
zeroIBD(s, ids = cous)
# Re-compute with nonzero threshold
zeroIBD(s, ids = cous, threshold = 1, unit = "cm")
zeroIBD(s, ids = cous, threshold = 1, unit = "mb")
[Package ibdsim2 version 2.0.0 Index]