reSNP: testing association between a SNP and phenotype

In ykim03517/reSNP: An efficient integrative resampling method for gene-trait association analysis

Description

Testing association between a SNP and phenotype

Usage

reSNP(data, grid = 0.01, R = 10^4, testStat = "score",
  out_type = "D", boot = FALSE, boot_Num = NULL, method_se = NULL,
  alpha_CI = NULL)

Arguments

data	a data set consists of phenotype, genotype under additive genetic model assumption, genotype expanded with grid interval, and covariate if applicable.
grid	an interval of grid search (default=0.01; range: 0<grid<1). A lower value of grid gives denser intervals.
R	a numeric value of the number of resampling replications.
testStat	a character value of a statistical test statistic (default='score'). 'LRT' indicates likelihood ratio test; 'score' means score test.
out_type	a character value of outcome type (default='D'). 'D' indicates dichotomous phenotype; 'C' represents continuouse phenotype.
boot	a logical value indicating whether to use bootstrap for confidence interval of the estimated genetic model.
boot_Num	a numeric value of bootstrap replications.
method_se	a method to compute standard error (default='percentile'). Users must choose a method in c('standard', 'percentile', 'BC', 'BCa'). 'standard' calculates a standard error of the bootstrap samples. 'percentile' uses percentiles of the bootstrap distribution to define the percentile confidence limits. 'percentile' method corrects for non-normality of the estimator of interest. 'BC' is a Bias-Corrected percentile method which corrects for narrowness bias of percentile CIs. The bias-correction factor isestimated using the inverse cdf of standard normal distribution. 'BCa' is a bias-corrected and accelerated percentaile method which corrects for narrowness bias and for nonconstant standard error of the estimator of interest (acceleration). The acceleration factor estimates the rate of change of the standard error of the estimator.
alpha_CI	a significance level (default=0.05).

Value

a list of p-value, estimated genetic model, a confidence interval of the estimated genetic model.

Author(s)

Yeonil Kim

ykim03517/reSNP documentation built on Nov. 5, 2019, 1:20 p.m.