CAST: CAST: Cohort Allelic Sums Test

In AssotesteR: Statistical Tests for Genetic Association Studies

Description

CAST is a pooled association test applied to discover if the difference in the sums of allelic mutation frequencies in case and control cohorts is greater than would be expected by chance. CAST works by first collapsing the genotypes across rare variants to generate a super-variant. It then tests the association between the trait and this new super-variant.

Usage

  CAST(y, X, maf = 0.05,  test = "fisher")

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
maf	numeric value indicating the minor allele frequency threshold for rare variants (maf=0.05 by default)
test	character string indicating the type of test to be applied. Possible values are "fisher" and "chisq" (test="fisher" by default)

Details

If no variants are below the specified maf threshold, the function will stop and return an error message

The argument test="fisher" involves a fisher exact test. Conversely, test="chisq" indicates a chi-square test.

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:

cast.stat	cast statistic
asym.pval	asymptotic p-value
args	descriptive information with number of controls, cases, variants, maf, and applied test
name	name of the statistic

Author(s)

Gaston Sanchez

References

Morgenthaler S, Thilly WG (2007) A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: A cohort allelic sums test (CAST). Mutation Research, 615: 28-56

See Also

link{TTEST}

Examples

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

  # number of controls
  controls = 500

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

  # phenotype vector
  phenotype = c(rep(1,cases), rep(0,controls))

  # genotype matrix with 10 variants (random data)
  set.seed(1234)
  genotype = matrix(rbinom(total*10, 2, 0.051), nrow=total, ncol=10)
 
  # apply CAST with fisher exact test 
  mycast1 = CAST(phenotype, genotype, maf=0.05, test = "fisher")
  mycast1

  # apply CAST with chi-square test 
  mycast2 = CAST(phenotype, genotype, maf=0.05, test = "chisq")
  mycast2
  
## End(Not run)

Example output

Loading required package: mvtnorm

 	 CAST: Cohort Allelic Sums Test 

Info: 
   cases  controls  variants   rarevar       maf      test  
     500       500        10         5      0.05    fisher  

cast.stat   asym.pval   
 0.886398    0.393446   

 	 CAST: Cohort Allelic Sums Test 

Info: 
   cases  controls  variants   rarevar       maf      test  
     500       500        10         5      0.05     chisq  

cast.stat   asym.pval   
 0.728310    0.393431   

AssotesteR documentation built on May 2, 2019, 3:55 a.m.