scHOT_calculateGlobalHigherOrderFunction — scHOT_calculateGlobalHigherOrderFunction • scHOT

this calculates the global higher order function and stores it in the output if these aren't found in the params slot then they need to be specified here

scHOT_calculateGlobalHigherOrderFunction(
  scHOT,
  higherOrderFunction = NULL,
  higherOrderFunctionType = NULL
)

Arguments

scHOT	A scHOT object
higherOrderFunction	A function object indicating the higher order function
higherOrderFunctionType	is "weighted" or "unweighted", determines if there is a weighting argument in the higher order function

Value

A scHOT object with scHOT_output$globalHigherOrderFunction in slot scHOT_output saved

Details

Calculates the global higher order function

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