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Use haplotype nearest neighbourhoods and other information returned by CladeMat() to efficiently remove structure corresponding to singletons or called sprigs from clade matrix 'M'

Usage

PruneCladeMat(M, neigh, sprigs, prune = "singleton.info", from_recipient = 1L)

Arguments

M

clade matrix such as that updated by CladeMat()

neigh

a list of nearest neighborhoods as retuned by CladeMat()

sprigs

a sprigs object as returned by Sprigs()

prune

a character indicating the type of information to be removed from the CladeMat(). See Details.

from_recipient

haplotype index at which to start trace calculation — useful for distributed computation (experimental feature, more documentation to come)

Value

There is nothing returned.

NOTE: for performance reasons, M is updated in-place.

References

Christ, R.R., Wang, X., Aslett, L.J.M., Steinsaltz, D. and Hall, I. (2024) "Clade Distillation for Genome-wide Association Studies", bioRxiv 2024.09.30.615852. Available at: doi:10.1101/2024.09.30.615852 .

Examples

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