get_thresh_simstat: Significance Threshold Estimation for Admixture Mapping using...

In kegrinde/STEAM: Significance Threshold Estimation for Admixture Mapping

Significance Threshold Estimation for Admixture Mapping using Test Statistic Simulation

Description

Compute genome-wide significance (test statistic or p-value) threshold for admixture mapping by simulating admixture mapping test statistics from their joint asymptotic distribution under the null (see Grinde et al., 2018) and finding the threshold that controls the empirical family-wise error rate.

Usage

get_thresh_simstat(g, map, props, nreps = 10000, alpha = 0.05,
  type = "pval")

Arguments

g	the generations since admixture.
map	data frame with m rows and at least 2 columns ('chr' containing chromosome number and 'cM' containing genetic position in centimorgans), where m = no. markers
props	data frame (n x K) of admixture proportions, where n = no. individuals and K = no. ancestral populations
nreps	the number of repetitions for the simulation study; default is 10000.
alpha	the level for family-wise error rate control; default is 0.05.
type	the type of threshold that should be returned: "stat" for test statistic or "pval" for p-value; defaults to pval.

Value

A single number indicating the estimated significance threshold (either test statistic or p-value).

Examples

get_thresh_simstat(g = 6, map = example_map, props = example_props, nreps = 10)
get_thresh_simstat(g = 6, map = example_map, props = example_props, nreps = 10, type="stat")

kegrinde/STEAM documentation built on June 30, 2024, 11:27 p.m.