scHOT_calculateGlobalHigherOrderFunction {scHOT} | R Documentation |
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 )
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 |
Calculates the global higher order function
A scHOT object with scHOT_output$globalHigherOrderFunction in slot scHOT_output saved
data(MOB_subset) sce_MOB_subset <- MOB_subset$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")