scHOT_setPermutationScaffold

Set permutation scaffold

scHOT_setPermutationScaffold(
  scHOT,
  numberPermutations = 1000,
  numberScaffold = 100,
  storePermutations = TRUE
)

Arguments

scHOT

A scHOT object

numberPermutations

The number of permutations, set as 1000 by default

numberScaffold

The number of scaffold, set as 100 by default, minimum 6. if you want all combinations to do permutations then set, numberScaffold much higher than the testingScaffold

storePermutations

a logical flag on whether Permutations should be stored, or discarded once used

Value

A scHOT object with storePermutations in slot scHOT_output saved

Examples

 data(MOB_subset)
 sce_MOB_subset <- MOB_subset$sce_MOB_subset
 scHOT_spatial <- scHOT_buildFromSCE(sce_MOB_subset,
                                     assayName = "logcounts",
                                    positionType = "spatial",
                                     positionColData = c("x", "y"))
pairs <- matrix(c("Arrb1", "Mtor", "Dnm1l", "Gucy1b3"), ncol = 2, byrow = TRUE)
rownames(pairs) <- apply(pairs,1,paste0,collapse = "_")
scHOT_spatial <- scHOT_addTestingScaffold(scHOT_spatial, pairs)
scHOT_spatial <- scHOT_setWeightMatrix(scHOT_spatial,
                                       positionColData = c("x","y"),
                                        positionType = "spatial",
                                        nrow.out = NULL,
                                        span = 0.05)
#> weightMatrix not provided, generating one using parameter settings...
scHOT_spatial <- scHOT_calculateGlobalHigherOrderFunction(
  scHOT_spatial,
  higherOrderFunction = weightedSpearman,
  higherOrderFunctionType = "weighted")
#> higherOrderFunctionType given will replace any stored param
#> higherOrderFunction given will replace any stored param
scHOT_spatial <- scHOT_setPermutationScaffold(scHOT_spatial,
                                              numberPermutations = 100)
#> numberScaffold set higher than the scaffold, setting permutation number for all tests