Indiv_Score_Test_Region: Score test for individual variants in a given variant-set

In xihaoli/STAAR: STAAR Procedure for Dynamic Incorporation of Multiple Functional Annotations in Whole-Genome Sequencing Studies

Score test for individual variants in a given variant-set

Description

The Indiv_Score_Test_Region function takes in genotype and the object from fitting the null model to analyze the associations between a quantitative/dichotomous phenotype and all individual variants in a given variant-set by using score test.

Usage

Indiv_Score_Test_Region(
  genotype,
  obj_nullmodel,
  rare_maf_cutoff = 0.01,
  rv_num_cutoff = 2
)

Arguments

genotype	an n*p genotype matrix (dosage matrix) of the target sequence, where n is the sample size and p is the number of genetic variants.
obj_nullmodel	an object from fitting the null model, which is the output from either fit_null_glm function for unrelated samples or fit_null_glmmkin function for related samples. Note that fit_null_glmmkin is a wrapper of the glmmkin function from the GMMAT package.
rare_maf_cutoff	the cutoff of maximum minor allele frequency in defining rare variants (default = 0.01).
rv_num_cutoff	the cutoff of minimum number of variants of analyzing a given variant-set (default = 2).

Value

A data frame with p rows corresponding to the p genetic variants in the given variant-set and three columns: Score (the score test statistic), SE (the standard error associated with the score test statistic), and pvalue (the score test p-value). If a variant in the given variant-set has minor allele frequency = 0 or greater than rare_maf_cutoff, the corresponding row will be NA. If a variant in the given variant-set has standard error equal to 0, the p-value will be set as 1.

References

Chen, H., et al. (2016). Control for population structure and relatedness for binary traits in genetic association studies via logistic mixed models. The American Journal of Human Genetics, 98(4), 653-666. (pub)

xihaoli/STAAR documentation built on Jan. 27, 2024, 8:51 a.m.