testAssoDist: Test the association between a comparator distance matrix,...
In perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data

Description Usage Arguments Value See Also

This function calculates and tests the association between a comparator distance matrix, based on any pairwise distance measure, and the reconstructed dendrograms across a genomic region of interest usingassociation measures such as the dCor statistic, HHG statistic, Mantel statistic, and RV coefficient. See the section Applications in vignette("perfectphyloR") for the detailed example.

1 2	testAssoDist(rdend, cdmat, method, hapMat, nperm = 0, xlab = "", ylab = "", main = "")

`rdend`	A `multiPhylo` object of reconstructed dendrograms at each focal SNV.
`cdmat`	A comparator matrix of pairwise distances (e.g. pairwise distances between haplotypes of a comparator dendrogram).
`method`	Association measures. Use "dCor" for dCor test, "HHG" for HHG test, "Mantel" for mantel test, and "RV" for RV test.
`hapMat`	An object of class `hapMat` containing SNV haplotypes.
`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).

A list with the following components:

`Stats`	A vector of observed statistics computed from the user-provided distance association method.
`OmPval`	A permutation-based omnibus P value for the test of any association across the genomic region using the maximum statistic over the genomic region as the test statistic.
`mPval`	A vector of marginal P values at each SNV position.
`plt`	A plot of the association profile over SNV locations in the region of interest.