compareSH: Compare Selection Coefficients and Dominance between...

In ThomasTaus/poolSeq: Simulate and Analyze Pool-seq Data

Description

compareSH tests the nullhypothesis that replicated allele frequency trajectories were generated with identical selection coefficients (s) and dominance (h).

Usage

compareSH(traj, t, Ne, haploid = FALSE, h = NA, N.ctraj = 10000, N.pval = 1000, cov = NA, method = c("LLS", "NLS", "automatic"))

## S3 method for class 'compsh'
print(x, ...)

Arguments

x	object of class "compsh" as returned by compareSH.
traj	numeric matrix of allele frequency trajectories, where columns correspond to individual time points
t	numeric vector indicating the number of generations for each column in traj.
Ne	numeric specifying the effective population size
haploid	logical indicating wether a population of haploid (haploid = TRUE) or diploid (default) individuals should be simulated.
h	numeric defining the dominance that should be assumed. If h = NA (default) dominance will be estimated alongside with the selection coefficient.
N.ctraj	numeric determining the number of simulations that should be performed to correct for bias in the consensus trajectory (by default sim = 10000).
N.pval	integer; the number of simulations performed to estimate the p-value (by default N.pval = 1000).
cov	numeric matrix of sequence coverages, where columns and rows correspond to measurement time points and replicates, respectively
method	character string defining the method that should be used to estimate s (and p0 or h).
...	currently not used.

Value

A list with class "compsh" containing the following components:

traj	matrix with observed allele frequency trajectories.
t	generations of each measurement time point.
Ne	effective population size.
haploid	logical for diploid or haploid individuals.
ctraj	consensus trajectory used to estimate s and h.
N.ctraj	number of simulations to correct 'ctraj' from bias.
s	estimated common s.
s.sep	individual estimates of s, one for each replicate.
h	if h == NA, estimated common h.
h.sep	individual estimates of h, one for each replicate.
h.given	dominance defined in h.
cov	matrix with observed sequence coverages.
s.p.value	p-value for s.
h.p.value	p-value for h.
N.pval	number of simulations to estimate p-value(s).

Author(s)

Thomas Taus

See Also

estimateSH

Examples

# simulate allele frequency trajectories under constant selection coefficient (and dominance)
tp <- seq(0, 100, by=10)
Ne <- 1000
traj <- wf.traj(p0=rep(0.05, times=3), Ne=Ne, t=tp, s=0.1, h=0.5, haploid=FALSE)

# test the null hypothesis that selection coefficients are identical between replicates
compareSH(traj=traj, t=tp, Ne=Ne, haploid=FALSE, N.pval = 100, h=0.5) ##### takes about 15 sec #####

ThomasTaus/poolSeq documentation built on Feb. 17, 2020, 1:52 p.m.