cape (version 2.0.2)

genome.wide.threshold.1D: Calculate a genome-wide significance threshold for the single-variant scan

Description

This function uses permtuation testing to calculate a genome-wide significance threshold for the single-variant scan. Significant standardized effect sizes are calculated based on user-defined alpha values. In each permutation, the phenotype or eigentrait is shuffled and all markers are retested with the permuted phenotype. The regression coefficients are collected from each permutation and the extreme value distribution is used to determine thresholds for the user-defined alpha values.

Usage

genome.wide.threshold.1D(data.obj, geno.mat, n.perm = 1000, 
alpha = c(0.01, 0.05), scan.what = c("eigentraits", "raw.traits"), 
verbose = FALSE)

Arguments

data.obj

The object in which all results are stored. See read.population.

geno.mat

The genotype matrix to be used in testing.

n.perm

The number of permutations to perform. The default is 1000.

alpha

A vector of alpha values for which significant standardized effect sizes should be calculated. Default values are 0.05 and 0.01.

scan.what

A character value that uniquely specifies whether the eigentraits or phenotypes should be scanned.

verbose

A logical value specifying whether the progress of the scan should be printed to the screen. A value of TRUE causes the progress to be printed to the screen.

References

Carter, G. W., Hays, M., Sherman, A., & Galitski, T. (2012). Use of pleiotropy to model genetic interactions in a population. PLoS genetics, 8(10), e1003010. doi:10.1371/journal.pgen.1003010

See Also

singlescan pairscan genome.wide.threshold.1D.parallel