Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1 |

`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 ( |

`weights` |
optional vector of weights for the variants ( |

`perm` |
positive integer indicating the number of permutations (100 by default) |

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.

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 |

Gaston Sanchez

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ```
## 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)
``` |

```
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
```

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