testDendAssoRI: Tests Rand Index between a comparator dendrogram and...

In perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data

Description

This function performs the Rand Index between a user-supplied comparator dendrogram and the reconstruced dendrograms at each focal SNV position in a genomic region. See the section Applications in vignette("perfectphyloR") for the detailed example.

Usage

testDendAssoRI(rdend, cdend, hapMat, k = 2, nperm = 0, xlab = "",
  ylab = "", main = "")

Arguments

rdend	A multiPhylo object of reconstructed dendrograms at each focal SNV.
cdend	A phylo object of the comparator dendrogram.
hapMat	An object of class 'hapMat'containing SNV haplotypes.
k	An integer that specifies the number of clusters that the dendrogram should be cut into. The default is k=2. Clusters are defined by starting from the root of the dendrogram and moving towards the tips, cutting horizontally at any given point in the dendrogram.
nperm	Number of permutations for the test of any association across the genomic region of interest. The default is 'nperm = 0';i.e., association will not be tested.
xlab	An optional character string for the label on the x-axis in the plot that is returned (none by default).
ylab	An optional character string for the label on the y-axis in the plot that is returned (none by default).
main	An optional character string for title in the plot that is returned (none by default).

Value

A list with the following components:

Stats	A vector of observed Rand indices.
OmPval	A permutation-based omnibus P value for the test of any association across the genomic region using the maximum Rand index over the genomic region as the test statistics.
mPval	A vector of marginal P values at each SNV position.
plt	A plot of the association profile of Rand indices over SNV locations in the region of interest.

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