scHOT_setPermutationScaffold {scHOT} | R Documentation

## 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)

[Package scHOT version 1.2.0 Index]