scHOT_calculateHigherOrderTestStatistics {scHOT} | R Documentation

## scHOT_calculateHigherOrderTestStatistics

### Description

Calculate and store the higherOrderSequence and higherOrderTestStatistic

### Usage

    scHOT_calculateHigherOrderTestStatistics(
      scHOT,
      higherOrderSummaryFunction = stats::sd,
      ...
    )

### Arguments

`scHOT` | A scHOT object
`higherOrderSummaryFunction` | A function which indicates how the higher order sequence is summarised, default is sd
`...` | parameters for higherOrderSummaryFunction

### Value

scHOT A scHOT object with results stored in scHOT_output slot

### 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")
    scHOT_spatial <- scHOT_setPermutationScaffold(scHOT_spatial,
                                                  numberPermutations = 100)
    scHOT_spatial <- scHOT_calculateHigherOrderTestStatistics(
      scHOT_spatial,
      higherOrderSummaryFunction = sd)

[Package scHOT version 1.6.0 Index]