scHOT_setWeightMatrix

Create scHOT object from a SingleCellExperiment object

scHOT_setWeightMatrix(
  scHOT,
  weightMatrix = NULL,
  positionType = NULL,
  positionColData = NULL,
  nrow.out = NULL,
  averageAcrossTrajectoryTies = FALSE,
  ...
)

Arguments

scHOT	A scHOT object
weightMatrix	A matrix indicating the weight matrix for scHOT analysis, such as the output from `trajectoryWeightMatrix` or `spatialWeightMatrix`. If this is not NULL then other parameters are ignored.
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
...	parameters for function trajectoryWeightMatrix or spatialWeightMatrix

Value

A scHOT object with slot weightMatrix 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)
#> weightMatrix not provided, generating one using parameter settings...