assoTest: Compute the user-provided association statistics

In perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data

Description

This function computes the user-given association statistics and return the association profile over a genomic region.

Usage

assoTest(Dx, Dy, hapMat, nperm, method, xlab = "", ylab = "",
  main = "")

Arguments

Dx	A numeric matrix of pairwise distances.
Dy	A second numeric matrix of pairwise distances.
hapMat	An object of hapMat.
nperm	The number of times to permute the rows and columns of Dy.
method	Association methods. Use "HHG" for HHG test, "dCor" for dCor test, "Mantel" for mantel test, "RV" for RV test.
xlab	An optional character string for the label on the x-axis(none by default).
ylab	An optional character string for the label on the y-axis(none by default).
main	An optional character string for title(none by default).

Value

A list of permutation p-values, corresponding statistics and a plot of association profile over SNV location.

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