perfectphyloR (version 0.2.1)

makePartition: Recursively partition haplotype matrix

Description

This function recursively partitions the SNVs in the window around the focal SNV.

Usage

makePartition(hapmat, splitSNV)

Arguments

hapmat

A hapMat object with SNVs ordered according to ancestry.

splitSNV

The index of the SNV where the haplotype matrix from orderSNVs is partitioned.

Value

A nested partition of haplotypes, implemented as a list of nodes, each with two child nodes.

Details

This function makes two clades based on splotSNV. For each partition, update splitSNV and use it to define subclades. Then, continue recursive partitioning until each partition has only one haplotype, or there are no more SNVs to consider.

See Also

makeDend, newNode, noVariation

Examples

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