Description Usage Arguments Value Examples
View source: R/reconstructPPregion.R
This function reconstructs perfect phylogenies on each possible focal SNV across a genomic region.
1 | reconstructPPregion(hapMat, minWindow, posn.lb = NULL, posn.ub = NULL)
|
hapMat |
A data structure of class |
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 |
posn.ub |
Upper bound of the subregion of |
An object of class multiPhylo
that contains multiple phylo
objects.
1 2 3 4 5 6 7 8 9 | 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)
|
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