CoMM

Source: R/RcppExports.R

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

CoMM_S2_testing(stringname1, stringname2, stringname3, stringname4,
  stringname5, bw, lam)

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

Value

List of model parameters

Details

CoMM_S2_testing fits the CoMM 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 = "";
lam = 0.95;
bw = 500000;

fm = CoMM_S2_paral_testing(file1,file2,file3, file4,file5, bw, lam);

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