hapnumtest: Iterative testing for the number of selected haplotypes.

In xthchen/haplotest: Haplotype based testing for evolve and resequence

Iterative testing for the number of selected haplotypes.

Description

This is the post-hoc test for testing for the number of selected haplotypes. The test should only be performed if haplotype based test have shown evidence of selection.

Usage

hapnumtest(
  frequency_matrix,
  p_combine_method = "omnibus",
  deltat = 10,
  Ne = 1000,
  repli = 1,
  seed = 2022
)

Arguments

frequency_matrix	Numeric matrix, with each i,j element being the frequency of haplotype i at sequenced time point j.
p_combine_method	Factor, method of pvalue combination, can be "omnibus" (Futschik, A. et al. 2019), "harmonic" (Wilson, D.J. (2019)), "vovk" (Vovk, V. et al. 2018), "bonferroni", "BH" (Benjamini & Hochberg 1995).
deltat	Numeric, number of generations between each pair of time points of interests
Ne	Numeric vector with length as number of replicates, containing information of Ne (effective population size) at each replicated population. If Ne changes over time, take as input a numeric matrix, with the column being the replicate position, row being the Ne at each sequenced time points.
repli	Numeric, specifying the number of replicated populations.
seed	setting seed of the run

Value

A number specifying the number of selected haplotypes.

See Also

haplotest()

Examples

#We show here an example for the test for the number of selected haplotypes
#Suppose we have the haplotype frequency matrix hap_freq, sequenced at every 10 generations, with effective population size 1000 and 3 replicate populations, using omnibus test as multiple testing correction, the number of selected haplotypes is computed by:
hap_num = hapnumtest(hap_freq, p_combine_method = "omnibus", deltat = 10, Ne = rep(1000,3), repli = 3)

xthchen/haplotest documentation built on Nov. 29, 2022, 12:07 p.m.