selectWindow: Select a window of SNVs about the focal SNV.

In perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data

Description

This internal function first identifies as many compatible SNVs as possible around the focal SNV. If the neighborhood of compatible SNVs is smaller than a user-defined minimum number of SNVs, this function expands the neighborhood by including incompatible SNVs in order of proximity to the focal SNV using the algorithm of Mailund et al. (2006). Then the function subsets the columns of the hapMat data object according to the resulting SNV window.

Usage

selectWindow(hapMat, focalSNV, minWindow)

Arguments

hapMat	hapMat data object.
focalSNV	The column number of the focal SNV in the hapMat data object.
minWindow	Minimum window size of the SNV neighborhood.

References

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

See Also

reconstructPP, findSNVs, subsetHapMat

Examples

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