AssotesteR (version 0.1-10)

CAST: CAST: Cohort Allelic Sums Test

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)

Value

"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

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.

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)