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.
testAssoDist(rdend, cdmat, method, hapMat, nperm = 0, xlab = "",
ylab = "", main = "")A multiPhylo object of reconstructed dendrograms at each focal SNV.
A comparator matrix of pairwise distances (e.g. pairwise distances between haplotypes of a comparator dendrogram).
Association measures. Use "dCor" for dCor test, "HHG" for HHG test, "Mantel" for mantel test, and "RV" for RV test.
An object of class hapMat containing SNV haplotypes.
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.
An optional character string for the label on the x-axis in the plot that is returned (none by default).
An optional character string for the label on the y-axis in the plot that is returned (none by default).
An optional character string for title in the plot that is returned (none by default).
A list with the following components:
A vector of observed statistics computed from the user-provided distance association method.
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.
A vector of marginal P values at each SNV position.
A plot of the association profile over SNV locations in the region of interest.