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