scHOT_setPermutationScaffold: scHOT_setPermutationScaffold

In shazanfar/scHOT: single-cell higher order testing

scHOT_setPermutationScaffold

Description

Set permutation scaffold

Usage

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)
scHOT_spatial <- scHOT_calculateGlobalHigherOrderFunction(
  scHOT_spatial,
  higherOrderFunction = weightedSpearman,
  higherOrderFunctionType = "weighted")
scHOT_spatial <- scHOT_setPermutationScaffold(scHOT_spatial,
                                              numberPermutations = 100)

shazanfar/scHOT documentation built on June 29, 2023, 5:29 p.m.