CoMM — CoMM_testing

CoMM to dissecting genetic contributions to complex traits by leveraging regulatory information.

CoMM_testing_run(stringname1, stringname2, stringname3, stringname4,
  stringname5, whCol, bw)

Arguments

stringname1	prefix for eQTL genotype file with plink format (bim, bed).
stringname2	prefix for GWAS genotype and phenotype file with plink format (bim, bed, fam).
stringname3	gene expression file with full name.
stringname4	covariates file for eQTL data.
stringname5	covariates file for GWAS data, e.g. top 10 PCs.
whCol	specify which phenotype is used in fam. For example, when whCol = 2, the seven-th column of fam file will be used as phenotype.
bw	the number of downstream and upstream SNPs that are considered as cis-SNP within a gene.

Value

List of model parameters

Details

CoMM_testing_run fits the CoMM model. It requires to provide plink binary eQTL genotype file (bim, bed) the GWAS plink binary file (bim, bed, fam), gene expression file for eQTL.

Author

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

Examples

##Working with no summary statistics, no covariates and options
file1 = "1000G.EUR.QC.1";
file2 = "NFBC_filter_mph10";
file3 = "Geuvadis_gene_expression_qn.txt";
file4 = "";
file5 = "pc5_NFBC_filter_mph10.txt";
whichPheno = 1;
bw = 500000;

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