A rare variant association test that utilizes protein tertiary structure to increase signal and to identify likely causal variants. Performs structure-guided collapsing, which leads to local tests that borrow information from neighboring variants on a protein and that provide association information on a variant-specific level.
point(yy, X, snp, proteinCoord, ..., trait = "binomial", cValues = c(0,
0.1, 0.2, 0.3, 0.4, 0.5), weighted = TRUE, weight = NULL,
kernel = "linear", d = NULL, pvMethod = "davies",
nperturb = 1000, verbose = TRUE)Returns a matrix the rows of which correspond to individual markers.
Columns correspond to:
(1) minP statistic;
(2) local kernel test p-value;
(3) optimal scale value from input cValues;
(4) minor allele frequency; and
(5) single variant score test p-value.
numeric vector; phenotype values.
numeric matrix; non-genetic covariates.
numeric matrix; genotype snp matrix (count of minor alleles). Matrix cannot contain missing values.
numeric matrix; columns correspond to 3 dimensional coordinates (x,y,z) of each variant in the protein tertiary structure.
optional additional arguments for p-value methods CompQuadForm::davies and CompQuadForm::liu.
character; type of phenotype data. Must be one of {'gaussian','binomial'} quantitative or case control data, respectively.
numeric vector; c values from which to choose the optimal neighborhood size for borrowing significant information.
logical; whether or not to weight the local kernel test using (non-distance based) weights.
numeric vector (optional) If NULL and weighted is TRUE (1.0-MAF)^24. Ignored if weighted is FALSE.
character; type of local kernel to use; Must be one of {'burden', 'linear', 'polynomial'}.
numeric; If kernel = 'poly', d is the order of the polynomial kernel.
character; method of calculating the p-value of each single marker test for fixed c values. Must be one of {'davies', 'liu'}.
numeric, number of perturbations/resamples (perturbed test statistics) to calculate p-value of minP statistic.
logical; generate progress screen prints.