CoMM

CoMM_S2 to dissecting genetic contributions to complex traits by leveraging regulatory information using GWAS summary data.

CoMM_S2_paral_testing(stringname1, stringname2, stringname3, stringname4,
  stringname5, bw, lam, coreNum)

Arguments

stringname1	prefix for eQTL genotype file with plink format (bim, bed).
stringname2	summary data for GWAS.
stringname3	prefix for reference panel file with plink forma (bim,bed).
stringname4	expression file for eQTL data.
stringname5	covariates file for eQTL data, e.g. top 10 PCs.
bw	the number of downstream and upstream SNPs that are considered as cis-SNP within a gene.
lam	shirnkage intensity for reference panel
coreNum	the number of cores in parallel running

Value

List of model parameters

Details

CoMM_S2_paral_testing fits the CoMM_S2 model. It requires to provide plink binary eQTL genotype file (bim, bed) the GWAS summary data, gene expression file for eQTL, reference panel data.

Author

Jin Liu, jin.liu@duke-nus.edu.sg

Examples

file1 = "1000G.EUR.QC.1";
file2 = "NFBC_beta_se_TG";
file3 = "1000G_chr_all"
file4 = "Geuvadis_gene_expression_qn.txt";
file5 = "";

bw = 500000;
lam = 0.95;
coreNum = 24;

fm = CoMM_S2_paral_testing(file1,file2,file3, file4,file5, bw, lam, coreNum);
#> Error in CoMM_S2_paral_testing(file1, file2, file3, file4, file5, bw,     lam, coreNum): negative length vectors are not allowed