scHOT_performPermutationTest — scHOT_performPermutationTest • scHOT

Perform permutation test

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)
#> 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
scHOT_spatial <- scHOT_calculateHigherOrderTestStatistics(
  scHOT_spatial,
  higherOrderSummaryFunction = sd)
#> higherOrderSummaryFunction will replace any stored param

scHOT_spatial <- scHOT_performPermutationTest(
  scHOT_spatial,
  verbose = TRUE,
  parallel = FALSE)
#> Permutation testing combination 1 of 2...
#> Permutation testing combination 2 of 2...