checkCompatible: Apply Four-Gamete Test to check the compatibility of a pair...

In perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data

Description

This function applies the four-gamete test to the pair of SNVs defined next SNV with each SNV in current neighborhood, to check the compatability.

Usage

checkCompatible(current, nextSNV, hapmat)

Arguments

current	Current SNVs in the neighborhood. This starts from the focal SNV.
nextSNV	A SNV whose compatability with each SNV in the current neighborhood needs to be checked.
hapmat	A matrix of 0's and 1's, with rows representing haplotypes and columns representing SNVs.

Value

A logical vector of the same length as current with entries being TRUE if next SNV is compatible with the corresponding SNV in current and FALSE other wise;returned to findSNVs

See Also

findSNVs, fourGamete

Examples

perfectphyloR documentation built on March 8, 2021, 9:06 a.m.