MAX3 {Rassoc} | R Documentation |
This function conducts the MAX3 test to a 2 by 3 case-control contingency table using either empirical or asymptotic methods. This test takes the maximum of the absolute values of the Cochran-Armitage trend tests optimal for recessive, additive/multiplicative and dominant models respectively.
MAX3(data, method, m)
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. |
method |
method is the approach used for calculating the p-value of MAX3 statistics. boot and bvn are empirical methods and asy is asymptotic method. |
m |
m is the replication times used for calculating the empirical p-values (boot and bvn). It can be any positive integer (1, for example) while choosing asymptotic method (asy). |
boot method re-samples case-control data under null hypothesis and applies MAX3 to each replicate. bvn directly generates statistics of MAX3 rather than case-control data under null hypothesis. asy calculates the p-value from the asymptotic distribution of MAX3 under null hypothesis.
method |
the method chosen to calculate the p-value of MAX3 |
statistic |
the statistic of the MAX3 test |
p.value |
the associated p-value of the MAX3 test |
Freidlin, B, Zheng, G, Li, Z and Gastwirth, JL (2002). Trend tests for case-control studies of genetic markers: power, sample size and robustness. Human Heredity 53, 146-152.
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).
library(Rassoc) ca=c(139,249,112) co=c(136,244,120) a=rbind(ca,co) MAX3(a,"boot",100000) ## The MAX3 test using the boot method ## data: a ## statistic = 0.5993, p-value = 0.7936 MAX3(a,"bvn",100000) ## The MAX3 test using the bvn method ## data: a ## statistic = 0.5993, p-value = 0.792 MAX3(a,"asy",1) ## The MAX3 test using the asy method ## data: a ## statistic = 0.5993, p-value = 0.7933