scHOT {scHOT} | R Documentation

## scHOT

### Description

A wrapper function to perform scHOT

### Usage

    scHOT(
      scHOT,
      testingScaffold = NULL,
      weightMatrix = NULL,
      positionType = NULL,
      positionColData = NULL,
      nrow.out = NULL,
      averageAcrossTrajectoryTies = FALSE,
      higherOrderFunction = NULL,
      higherOrderFunctionType = NULL,
      numberPermutations = 1000,
      numberScaffold = 100,
      storePermutations = TRUE,
      higherOrderSummaryFunction = sd,
      parallel = FALSE,
      BPPARAM = BiocParallel::SerialParam(),
      usenperm_estimate = FALSE,
      nperm_estimate = 10000,
      maxDist = 0.1,
      plot = FALSE,
      verbose = TRUE,
      ...
    )

### Arguments

`scHOT` | A scHOT object
`testingScaffold` | A matrix with rows for each testing combination
`weightMatrix` | A matrix indicates the weight matrix for scHOT analysis
`positionType` | A string indicating the position type, either "trajectory" or "spatial"
`positionColData` | Either trajectory or spatial information for each sample. If positionType is "trajectory" then positionColData should be a character or numeric indicating the subset of colData of the scHOT object. If positionType is "spatial" then positionColData should be a character or numeric vector indicating the subset of colData that give the full spatial coordinates.
`nrow.out` | The number of weightings to include for testing, a smaller value is faster for computation
`averageAcrossTrajectoryTies` | Logical indicating whether ties in the trajectory should be given the same local weights
`higherOrderFunction` | A function object indicates the higher order function
`higherOrderFunctionType` | is "weighted" or "unweighted", determines if there is a weighting argument in the higher order function
`numberPermutations` | The number of permutations, set as 1000 by default
`numberScaffold` | The number of testing scaffolds to perform permutations, set as 100 by default
`storePermutations` | a logical flag on whether permutation values should be saved
`higherOrderSummaryFunction` | A functon indicating the higher order summary function (default is standard deviation 'sd')
`parallel` | A logical input indicating whether to run the permutation test using multiple cores in parallel.
`BPPARAM` | A `BiocParallelParam` class object from the `BiocParallel` package is used. Default is SerialParam().
`usenperm_estimate` | Logical (default FALSE) if number of neighbouring permutations should be used to estimate P-values, or if difference of global higher order statistic should be used
`nperm_estimate` | Number of neighbouring permutations to use for p-value estimation
`maxDist` | max difference of global higher order statistic to use for p-value estimation (default 0.1)
`plot` | A logical input indicating whether the results are plotted
`verbose` | A logical input indicating whether the intermediate steps will be printed
`...` | parameters for function trajectoryWeightMatrix or spatialWeightMatrix

### Value

A scHOT object

### 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(scHOT_spatial,
                           testingScaffold = pairs,
                           positionType = "spatial",
                           positionColData = c("x", "y"),
                           nrow.out = NULL,
                           higherOrderFunction = weightedSpearman,
                           higherOrderFunctionType = "weighted",
                           numberPermutations = 100,
                           higherOrderSummaryFunction = sd,
                           parallel = FALSE,
                           verbose = TRUE,
                           span = 0.05)

[Package scHOT version 1.0.0 Index]