scHOT_calculateHigherOrderTestStatistics {scHOT} | R Documentation |
Calculate and store the higherOrderSequence and higherOrderTestStatistic
scHOT_calculateHigherOrderTestStatistics( scHOT, higherOrderSummaryFunction = stats::sd, ... )
scHOT |
A scHOT object |
higherOrderSummaryFunction |
A function which indicates how the higher order sequence is summarised, default is sd |
... |
parameters for higherOrderSummaryFunction |
scHOT A scHOT object with results stored in scHOT_output slot
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)