Cochran-Armitage test in R

Question

[alessandrotestori7]

Hi.

Is there a function in R to implement Cochran-Armitage test? I need to perform this test on allele frequencies.

Thanks.

Answer 1

[andrew.j.skelton73]

See the thread here

You'll need the Coin package.

library("coin")
lungtumor <- data.frame(dose = rep(c(0, 1, 2), c(40, 50, 48)),
                         tumor = c(rep(c(0, 1), c(38, 2)),
                                   rep(c(0, 1), c(43, 7)),
                                   rep(c(0, 1), c(33, 15))))
### linear-by-linear association test with scores 0, 1, 2
### is identical with Cochran-Armitage test
lungtumor$dose <- ordered(lungtumor$dose)
independence_test(tumor ~ dose, data = lungtumor, teststat = "quad",
                   scores = list(dose = c(0, 1, 2)))

        Asymptotic General Independence Test

data:  tumor by groups 0 < 1 < 2
T = 10.6381, df = 1, p-value = 0.001108

I've not tested this code, it's skimmed from the link.

[alessandrotestori7]

Thanks. There is something which is not clear to me, however: what is the meaning of c(40, 50, 48) in dose = rep(c(0, 1, 2), c(40, 50, 48) ?

[andrew.j.skelton73]

That's an example data frame to run the function. c(40, 50, 48) Are the number of repetitions of c(0, 1, 2), as it's wrapped in rep.

[zx8754]

[here] link is broken.

Answer 2

[dk364]

prop.trend.test() function does the same job.