catt: Cochrane armitage trend test (CATT) for SNP genotypes
In HapEstXXR: Multi-Locus Stepwise Regression

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

Performs chi-squared test for SNP genotypes. By default, score is chosen as the number of alleles (0, 1, 2).

1	catt(y, x, score = c(0, 1, 2))

`y`	Vector of trait values. `y` must have values of 1 for event, 0 for no event.
`x`	Vector of SNP genotypes, 1-column coding (SNP allele dosis: 0,1,2).
`score`	Group score.

The Cochran-Armitage trend test is typically used in categorical data analysis when some categories are ordered. Here it is used as a genotype-based test for candidate gene association.

`2x3-table`	Genotype distribution.
`chisq`	The value for the test statistic.
`df`	Degrees of freedom.
`p.value`	The p-value for the test.
`n.miss`	Number of individuals with missing values.

Sven Knueppel

Sasieni PD. From genotypes to genes: doubling the sample size.Biometrics. 1997 Dec;53(4):1253-61.

prop.trend.test

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y <- sample(c(0, 1), 100, replace = TRUE)
x <- sample(c(0, 1, 2), 100, replace = TRUE)
catt(y, x)

Loading required package: survival
$`2x3-table`
   0  1  2
0 18 18 20
1 15 15 14

$chisq
[1] 0.1256245

$df
[1] 1

$p.value
[1] 0.7230126

$n.miss
[1] 0