SCORE: SCORE: Score Test (from Logistic Regression)

In gastonstat/AssotesteR: Statistical Tests for Genetic Association Studies

Description

The Score test is one of the statistical tests used for logistic regression models, which is one of the standard approaches used in genetic association studies. Under the null hypothesis that there is no associated variants within the examined region, the test statistic has an asymptotic chi-square distribution. In addition, a permutation procedure can be applied to assess the significance of the test.

Usage

  SCORE(y, X, perm = 100)

Arguments

y	numeric vector with phenotype status: 0=controls, 1=cases. No missing data allowed
X	numeric matrix or data frame with genotype data coded as 0, 1, 2. Missing data is allowed
perm	positive integer indicating the number of permutations (100 by default)

Details

There is no imputation for the missing data. Missing values are simply ignored in the computations.

Value

An object of class "assoctest", basically a list with the following elements:

score.stat	score statistic
asym.pval	asymptotic p-value
perm.pval	permuted p-value
args	descriptive information with number of controls, cases, variants, and permutations
name	name of the statistic

Author(s)

Gaston Sanchez

References

Clayton D, Chapman J, Cooper J (2004) Use of unphased multilocus genotype data in indirect association studies. Genetic Epidemiology, 27: 415-428

Chapman J, Whittaker J (2008) Analysis of Multiple SNPs in a Candidate Gene or Region. Genetic Epidemioloy, 32: 560-566

See Also

SSU, SSUW, SUM

Examples

  ## Not run: 
  
  # number of cases
  cases = 500

  # number of controls
  controls = 500

  # total (cases + controls)
  total = cases + controls

  # phenotype (first column of genodata)
  phenotype = c(rep(1, cases), rep(0, controls))

  # genotype matrix with 10 variants (random data)
  set.seed(123)
  genotype = matrix(rbinom(total*10, 2, 0.05), nrow=total, ncol=10)

  # apply SCORE with 500 permutations
  myscore = SCORE(phenotype, genotype, perm=500)
  myscore
  
## End(Not run)

gastonstat/AssotesteR documentation built on May 16, 2019, 5:43 p.m.