perfectphyloR (version 0.2.1)

reconstructPP: Reconstruct the perfect phylogeny at a given focal SNV

Description

This function reconstructs the perfect phylogeny at a given focal SNV using the recursive partitioning algorithm of Gusfield (1991) on compatible SNVs, and the modification of Mailund et al. (2006) to include incompatible SNVs that are nearby.

Usage

reconstructPP(hapMat, focalSNV, minWindow = 1, sep = "-")

Arguments

hapMat

A data structure of class hapMat. Eg: created by the createHapMat function.

focalSNV

The column number of the focal SNV at which to reconstruct the reconstructed partitions.

minWindow

Minimum number of SNVs around the focal SNV in the window of SNVs used to reconstruct the partitions (default is the maximum of one and 2% of the total number of the SNVs).

sep

Character string separator to separate haplotype names for haplotypes that can not be distingushed in the window around the focal point. For example, if a tip is comprised of haplotypes "h1" and "h3", and sep = "-", then the tip label will be "h1-h3". The default value is "-". See details.

Value

An object of class phylo with indices of the column boundaries of the hapMat object that were used to reconstruct the partition in the window of SNVs.

Details

To reconstruct the perfect phylogeny from sequence data, these two steps are followed: (1) Select a window of SNVs at a given focal SNV. (2) Build the perfect phylogey for the window of SNVs. More details can be found in the references.

The following figure shows the reconstructed partitions at the tenth SNV position of ex_hapMatSmall_data.

References

Gusfield, D. (1991) Efficient algorithms for inferring evolutionary trees. Networks, 21(1), 19-28.

Mailund, T., Besenbacher, S., and Schierup, M. H. (2006) Whole genome association mapping by incompatibilities and local perfect phylogenies. BMC Bioinformatics, 7(1), 454.

Examples

# NOT RUN {
data(ex_hapMatSmall_data)

rdend <- reconstructPP(hapMat = ex_hapMatSmall_data,
                      focalSNV = 10,
                      minWindow = 1,
                      sep = "-")

# Plot the reconstructed perfect phylogeney.

plotDend(rdend, direction = "down")

# Extract the positions of the lower and upper limits of a window of SNVs in hapMat object 
# to reconstruct the partition, rdend.

ex_hapMatSmall_data$posns[rdend$snvWinIndices]
  
# }