scHOT_performPermutationTest {scHOT} | R Documentation

## scHOT_performPermutationTest

### Description

Perform permutation test

### Usage

    scHOT_performPermutationTest(
      scHOT,
      verbose = FALSE,
      parallel = FALSE,
      BPPARAM = BiocParallel::SerialParam()
    )

### Arguments

`scHOT` | A scHOT object
`verbose` | A logical input indicates whether the intermediate steps will be printed
`parallel` | A logical input indicates whether run the permutation test using multiple cores in parallel.
`BPPARAM` | A `BiocParallelParam` class object from the `BiocParallel` package is used. Default is SerialParam().

### Value

scHOT A scHOT object with results stored in scHOT_output slot

### 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)
    scHOT_spatial <- scHOT_calculateHigherOrderTestStatistics(
      scHOT_spatial,
      higherOrderSummaryFunction = sd)

    scHOT_spatial <- scHOT_performPermutationTest(
      scHOT_spatial,
      verbose = TRUE,
      parallel = FALSE)

[Package scHOT version 1.6.0 Index]