Run CACTI association test for a single chromosome
Usage
cacti_cal_p(
file_qtl_cis_norm,
chr,
file_peak_group,
file_pheno_cov_residual,
file_p_peak_group,
dir_pco = system.file("pco", package = "cacti"),
min_peaks = 2
)Arguments
- file_qtl_cis_norm
Path to cis QTL summary stats. Must contain columns: phe_id, var_id, z.
- chr
Chromosome label (e.g., "chr21"). Used to subset peak groups.
- file_peak_group
Path to peak-window metadata (groups) file. Produced by step_group_peak_window.
- file_pheno_cov_residual
Path to residualized phenotype matrix file. Produced by step_pheno_cov_residual.
- file_p_peak_group
Output path for per-window pvalues. Columns: group, snp, pval.
- dir_pco
Directory containing association test helpers: ModifiedPCOMerged_acat.R, liu.R, liumod.R, davies.R, qfc.so.
- min_peaks
Minimum number of peaks required in a group to run the multivariate PCO test (>= min_peaks -> PCO; < min_peaks -> univariate p).