estimateHeritability.RdThe function invokves GCTA in the system and estimates the germline heritability of a biomarker given cis-regions around the biomarker and any associated mediators of interest.
estimateHeritability( biomInt, snps, pheno, snpLocs, mediator, medLocs, covariates, fileName, dimNumeric, numMed = 5, cisDist = 5e+05, needMed = T, prune = F, medList, verbose = F, windowSize, numSNPShift, ldThresh, ldScrRegion = 200, LDMS = F, supplySNP = F, snpAnnot = NULL )
| biomInt | character, identifier for biomarker of interest |
|---|---|
| snps | data frame, SNP dosages |
| snpLocs | data frame, MatrixEQTL locations for SNPs |
| mediator | data frame, mediator intensities |
| medLocs | data frame, MatrixEQTL locations for mediators |
| covariates | data frame, covariates |
| fileName | character, throw away name for PLINK files |
| dimNumeric | integer, number of continuous covariates |
| numMed | integer, maximum number of mediators to find |
| cisDist | numeric, base pair window of cis definition |
| needMed | logical, T/F if the biomarker of interest has associated mediators |
| medList | character vector, vector of mediator names |
| verbose | logical, T/F for detailed output |
| windowSize | integer, window size for PLINK pruning |
| numSNPShift | integer, shifting window from PLINK pruning |
| ldThresh | numeric, maximum threshold for linkage disequilibrium |
| ldScrRegion | numeric, number of SNPs per bin in GCTA-LDMS |
| LDMS | logical, T/F to run GCTA-LDMS |
| supplySNP | logical, T/F to run GCTA on the full provided snps |
heritability estimate and associated LRT P-value