runGcdh: Run GCDH analysis
Description
Runs GCDH over the given PlGwasC object.
The PlGwasC object is first filtered by p-values from a plink --assoc run if a p-value threshold is given.
New PlGwasC objects are generated by shifting the PLINK bed file (e.g. shift1.bed, shift2.bed, ...) one by one.
A GWAS is run for each of these PlGwasC objects and results are collected into big.matrix files.
Usage
runGcdh(pl_gwas, n_shift, gwas_col_select = NULL, collapse_matrix = NULL, rm_shifted_files = TRUE, dist_threshold = 5e+05)
Arguments
n_shift
integer. Maximum shift number.
gwas_col_select
character. Columns to read from a GWAS output file. Default to collenv$.linear_header_default
collapse_matrix
matrix. 4 by 4 matrix used for generating collapsed genotypes.
rm_shifted_files
logical. Whether to remove shifted bed files after analysis is done.
dist_threshold
integer. SNPs beyond this distance will be ignored. Default to 500kb.
Value
A list with the following members: (1) the input PlGwasC object. (2) an info data frame with CHR, BP and SNP columns. (3) One big.matrix object for each of the names in gwas_col_select