scHOT_calculateGlobalHigherOrderFunction: scHOT_calculateGlobalHigherOrderFunction

In shazanfar/scHOT: single-cell higher order testing

scHOT_calculateGlobalHigherOrderFunction

Description

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

Usage

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

Details

Calculates the global higher order function

Value

A scHOT object with scHOT_output$globalHigherOrderFunction in slot scHOT_output saved

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")

shazanfar/scHOT documentation built on June 29, 2023, 5:29 p.m.