perfectphyloR (version 0.2.1)

reconstructPPregion: Reconstruct perfect phylogeny sequencce across a region

Description

This function reconstructs perfect phylogenies on each possible focal SNV across a genomic region.

Usage

reconstructPPregion(hapMat, minWindow, posn.lb = NULL, posn.ub = NULL)

Arguments

hapMat

A data structure of class hapMat. See the arguments in reconstructPP.

minWindow

Minimum number of SNVs around the focal SNV in the window of SNVs used to reconstruct the perfect phylogeny.

posn.lb

Lower bound of the subregion of hapMat (in base pairs) within which to consider SNVs.

posn.ub

Upper bound of the subregion of hapMat (in base pairs) within which to consider SNVs.

Value

An object of class multiPhylo that contains multiple phylo objects.

Examples

# NOT RUN {
data(ex_hapMatSmall_data)   
                   
# Reconstruct partitions across the region of ex_hapMatSmall_data.
rdends <- reconstructPPregion(hapMat = ex_hapMatSmall_data,
                      minWindow = 1)
                      
# Reconstruct partitions between a given range SNV positions.
rdends_range <- reconstructPPregion(hapMat = ex_hapMatSmall_data, minWindow = 1,
                                      posn.lb = 2000, posn.ub = 7000)                      

# }