runTypeI: Run simulations to control type-I error

Description

Simulate a new phenotype N times and run GCDH with each. The phe_fun function is used to generate new phenotype file. When this function is not given, the phenotype file from the PlGwasC object will be permuted and used as the new phenotype file (permutation analysis). Thus when no phe_fun is supplied, this function can be used to survey p-values under the null distribution. A threshold for Genome-wide significance can be calculated from these p-values by 5 any other alpha-level) quantile.

Usage

runTypeI(pl_gwas, n_shift, n_simu, phe_fun = NULL, dist_threshold = 5e+05, p_threshold = NULL, collapse_matrix = NULL, rm_shifted_files = TRUE)

Arguments

pl_gwas

PlGwasC object

n_shift

integer. n_shift for each GCDH run.

n_simu

integer. Number of simulations to run.

phe_fun

function. Used to generate new phenotype file.

dist_threshold

See runGcdh.

p_threshold

numeric or NULL. When it's not NULL, the PlGwasC object is filtered by assocFilter first.

collapse_matrix

See runGcdh.

rm_shifted_files

See runGcdh.

Value

A list with the following members: (1) tag of this simulation, can be used to remove related files. (2) a list of SNP pairs. If "snp_pair" is a member of the result from phe_fun, then this list will be non-empty, otherwise it will be empty. (3) a list of reports from all the GCDH analysis. (4) global minimal p-values of the single-SNP approach. (4) global minimal p-values of GCDH.