CATT {Rassoc} | R Documentation |
This function conducts the Cochran-Armitage trend test to a 2 by 3 case-control contingency table and reports the test statistics, associated p-value and conclusion for the hypothesis test respectively.
CATT(data, x)
data |
data is a 2 by 3 case-control contingency table. The first and second rows represent the case group and control group respectively. The first, second and third columns represent the genotypes of a susceptibility diallelic marker containing 0, 1 and 2 risk allele respectively. Thus, the numbers in this table represent the genotype counts belonging to the corresponding genotypes and case-control status. |
x |
x is the score of the Cochran-Armitage trend test. It can be any real number between 0 and 1. Specifically, x=0, 0.5 and 1 are optimal for recessive, additive/multiplicative and dominant genetic models respectively. |
statistic |
the statistic of the Cochran-Armitage trend test |
p.value |
the associated p-value of the Cochran-Armitage trend test |
Sasieni, PD(1997). From genotypes to genes: doubling the sample size. Biometrics 53, 1253-1261.
Zang Y, Fung WK and Zheng G(2009). Simple Algorithms to calculate the asymptotic null distribution for MAX3 and genetic model selection in case-control genetic association studies in R. Journal of Statistical software (revised).
Zheng, G, Freidlin, B, Li, Z and Gastwirth, JL (2003). Choice of scores in trend tests for case-control studies of candidate-gene associations. Biometrical Journal 45, 335-348.
library(Rassoc) data(caco) ex=matrix(caco[1,],nrow=2,byrow=TRUE) ## ex is an example of a 2 by 3 case-control contingency table. CATT(ex,0.5) ## Conduct the Cochran-Armitage trend test to dataset ex. x is chosen as 0.5, ##which is optimal under the additive/multiplicative genetic model. ## The Cochran-Armitage trend test ## data: ex ## statistic = -5.1171, p-value = 3.102e-07 ## The statistic of the test is -5.1171. ## The associated p-value of the test is 3.102e-07.