scHOT_calculateGlobalHigherOrderFunction {scHOT} | R Documentation

## 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")

[Package scHOT version 1.4.0 Index]