scHOT_buildFromSCE {scHOT} | R Documentation |
Create scHOT object from a SingleCellExperiment object
scHOT_buildFromSCE( sce, assayName = "counts", positionType = NULL, positionColData = NULL )
sce |
A SingleCellExperiment object |
assayName |
is a single assay to pull out from sce as the expression matrix input of scHOT |
positionType |
A string indicates the position type, either trajectory or spatial |
positionColData |
Strings indicate the position information stored in colData. If positionType is "trajectory" then positionColData should be a sortable vector if positionType is "spatial" then positionColData should be a matrix type object. |
A scHOT object
library(SingleCellExperiment) dat <- rbind(rnorm(50), rnorm(50), rnorm(50)) colnames(dat) <- paste0("cell_", 1:ncol(dat)) rownames(dat) <- c("gene_1","gene_2", "gene_2") sce <- SingleCellExperiment::SingleCellExperiment(assays = S4Vectors::SimpleList(counts = dat)) scHOT <- scHOT_buildFromSCE(sce)