CoMM — CoMM_S4_testing

CoMM_S4_testing_mt to dissecting genetic contributions to complex traits by leveraging regulatory information using both eQTL and GWAS summary statistics across whole genome data with multiple threads.

CoMM_S4_testing_mt(stringname1, stringname2, stringname3, stringname4,
  stringname5, px, lam, coreNum)

Arguments

stringname1	file for eQTL summary data file with the format described in the vignette.
stringname2	file for GWAS summary data file with the format described in the vignette.
stringname3	prefix for eQTL reference panel file with plink format (bim,bed).
stringname4	prefix for the file complement the information of SNPs in eQTL summary statistics with the format described in vignette
stringname5	prefix for GWAS reference panel file with plink format (bim,bed).
px	logical value(1 or 0) for indicating whether to use paramter expansion to accerate algorithm
lam	shirnkage intensity for reference panel
coreNum	the number of cores in parallel running

Value

List of model parameters

Details

CoMM_S4_testing_mt fits the CoMM_S4 model across whole genome with multiple threads. It requires to provide both the eQTL and GWAS summary data, two reference panel data for eQTL and GWAS data respectively.

Author

Yi Yang, gmsyany@nus.edu.sg

Examples


file1 = "cis-eQTLs_full_chr1_1-100000.txt";
file2 = "NFBC_ph1_beta_se.txt";
file3 = "all_chr_1000G"
file4 = "cis-eQTLs_full_chr1";
file5 = "all_chr_1000G";
px = 1;
lam = 0.95;
coreNum = 24

fm = CoMM_S4_testing_mt(file1,file2,file3, file4,file5, px, lam, coreNum);
#> begin to read reference panel
#> Error in CoMM_S4_testing_mt(file1, file2, file3, file4, file5, px, lam,     coreNum): Mat::col(): index out of bounds