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