Directionless omnibus test of a categorical focal exposure over a set

Pools the per-probe F statistic for the k - 1 contrast columns and calibrates it by the same block permutation the directional tests use. This answers "does this factor move the set at all" and gives up the direction, which is the property that separates DMSA from the methods it is compared against. Use it as a screen, or when the levels have no ordering and no reference level is defensible - and report dmsa_contrasts() alongside it.

Usage

dmsa_omnibus(data, Y, design, beta_input = TRUE, B = 999, seed = 1L)

Arguments

data: Analysis data frame.
Y: Probe matrix (subjects x probes), betas or M-values.
design: A dmsa_design whose focal_test names the factor.
beta_input: Passed through: are the columns of Y betas?
B: Permutations.
seed: RNG seed.

Value

A list with the pooled statistic, the permutation p-value, and an explicit directional = FALSE.

Examples

set.seed(1)
n <- 90
d <- data.frame(style = factor(sample(c("secure", "anxious", "avoidant"),
                                      n, TRUE)),
                age = rnorm(n), cID = rep(seq_len(n / 2), each = 2))
Y <- matrix(plogis(rnorm(n * 8)), n, 8)     # beta values for 8 probes
des <- dmsa_design(focal = "style", fixed = "age", exchangeable = "cID")
## three attachment styles with no defensible reference level: the pooled
## F asks only whether the factor moves the set, and gives up the direction
o <- dmsa_omnibus(d, Y, des, B = 99, seed = 5)
round(o$p_perm, 3)
#> [1] 0.73
o$directional    # always FALSE: a pooled F on 2 df has no sign
#> [1] FALSE