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

In kegrinde/STEAM: Significance Threshold Estimation for Admixture Mapping

Significance Threshold Estimation for Admixture Mapping using Analytic Approximation

Description

Compute genome-wide significance (test statistic or p-value) threshold for admixture mapping using analytic approximation to the family-wise error rate. For more details, see Grinde et al. (2019).

Usage

get_thresh_analytic(g, map, alpha = 0.05, type = "pval",
  searchint = c(1.96, 8))

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
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.
searchint	the range of test statistic thresholds for uniroot to search; defaults to 1.96–8, corresponding to p-value threshold of 0.05–1.2e-15

Value

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

See Also

uniroot for finding roots of functions

Examples

get_thresh_analytic(g = 6, map = example_map) # get p-value threshold
get_thresh_analytic(g = 6, map = example_map, type = "stat") # get test statistic threshold

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