scHOT_setPermutationScaffold {scHOT} | R Documentation |
Set permutation scaffold
scHOT_setPermutationScaffold( scHOT, numberPermutations = 1000, numberScaffold = 100, storePermutations = TRUE )
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 |
A scHOT object with storePermutations in slot scHOT_output saved
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)