Cell permutation tests (internal)

Cell permutation tests (internal)

.cluster_permute_test(
  labels,
  covariates,
  strata,
  statistic,
  contrasts,
  n_perm,
  alternative,
  ...
)

Arguments

labels

factor of length n

covariates

data.frame of length n

strata

factor

statistic

function of label (vector) and covariate (data.frame). If this returns a vector, then by default each level will be compared against each other, pairwise, but see the next section.

contrasts

an optional list of numeric vectors. Each will be dotted with the statistic, or optionally a matrix provided in which case each row would be tested one-by-one.

n_perm

number of permutations to run

alternative

character naming the direction statistic should be fall under the alternative hypothesis

...

passed along to statistic

Value

a list containing the observed value of the statistic, the permuted values of the statistic, its expectation (under independence), a p-value, and the Monte Carlo standard error (of the expected value).