perfectphyloR (version 0.2.1)

assoTest: Compute the user-provided association statistics

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.