findPattern: Find specific IBD patterns
In ibdsim2: Simulation of Chromosomal Regions Shared by Family Members

Description Usage Arguments Details Value Examples

Find segments satisfying a particular pattern of IBD sharing, in a list of IBD simulations

1	findPattern(sims, pattern)

`sims`	A `genomeSim` object, or a list of such. Typically made by `ibdsim()`.
`pattern`	A list of two vectors names `carriers` and `noncarriers`.

For each simulation, this function extracts the subset of rows satisfying the allele sharing specified by pattern. That is, segments where some allele occur in all of pattern$carriers, but in none of pattern$noncarriers.

A matrix (if sims is a single genomeSim object), or a list of matrices.

x = nuclearPed(3)
s = ibdsim(x, N = 1, map = uniformMap(M = 1), seed = 1729)
s1 = s[[1]]

# Segments where some allele is shared by 3 and 4, but not 5
pattern = list(carriers = 3:4, noncarriers = 5)
findPattern(s1, pattern)

# Visual confirmation:
haploDraw(x, s1, margin = c(5,3,3,3))