CMAT: CMAT: Cumulative Minor Allele Test

In AssotesteR: Statistical Tests for Genetic Association Studies

Description

CMAT is a pooling method proposed by Zawistowski et al (2010). CMAT works by comparing weighted minor-allele counts (for cases and controls) against the weighted major-allele counts (for cases and controls). Although the CMAT test statistic is based on a chi-square statistic, it does not follow a known distribution and its significance has to be determined by a permutation procedure.

Usage

  CMAT(y, X, maf = NULL, weights = NULL, 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
maf	optional numeric value to specify a threshold for the minor allele frequency of rare variants (NULL by default)
weights	optional vector of weights for the variants (NULL by default)
perm	positive integer indicating the number of permutations (100 by default)

Details

By default, argument maf=NULL meaning that no rare variants are selected

By default, argument weights=NULL but different values for the variants can be provided

Statistical significance is determined by permutation procedure

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:

cmat.stat	cmat statistic
perm.pval	permuted p-value
args	descriptive information with number of controls, cases, variants, rare variants, maf, and permutations
name	name of the statistic

Author(s)

Gaston Sanchez

References

Zawistowski M, Gopalahrishnan S, Ding J, Li Y, Grimm S, Zollner S (2010) The American Journal of Human Genetics, 87: 604-617

See Also

CMC, WSS

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 CMAT with 500 permutations
  mycmat1 = CMAT(phenotype, genotype, perm=500)
  mycmat1

  # apply CMAT with maf=0.05 and 500 permutations
  mycmat2 = CMAT(phenotype, genotype, maf=0.05, perm=500)
  mycmat2
  
## End(Not run)

Example output

Loading required package: mvtnorm

 	 CMAT: Cumulative Minor Allele Test 

Info: 
   cases  controls  variants   rarevar       maf   n.perms  
     500       500        10      NULL      NULL       500  

cmat.stat   perm.pval   
 1.145231    0.272000   

 	 CMAT: Cumulative Minor Allele Test 

Info: 
   cases  controls  variants   rarevar       maf   n.perms  
   5e+02     5e+02     1e+01     5e+00     5e-02     5e+02  

cmat.stat   perm.pval   
 0.863837    0.328000   

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