findSNVs: Find the window of SNVs at a focal point

In perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data

Description

This function identifies a window of compatible SNVs about the focal SNV.

Usage

findSNVs(hapMat, focalSNV, minWindow = 1)

Arguments

hapMat	hapMat data object.
focalSNV	The column number of the focal in the haplotype data matrix at which to reconstruct the dendrogram.
minWindow	Minimum window size of the SNV neighborhood.

Details

This function starts at the focal SNV, and tries expanding the neighborhood of compatible SNVs. This process is stopped when there are no more compatible SNVs to the left or right of the focal SNV. If the block of compatible SNVs does not have at least a user-defined minimum number of SNVs, this function expands the window to include incompatible SNVs.

Value

Return a list of SNVs in the window with their state of compatiblity to selectWindow.

See Also

selectWindow, checkCompatible, getnSNVs, getNextFromFocal, getNextLeftFocal, getNextRightFocal

Examples

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