scHOT_buildFromSCE {scHOT} | R Documentation

## scHOT_buildFromSCE

### Description

Create scHOT object from a SingleCellExperiment object

### Usage

    scHOT_buildFromSCE(
      sce,
      assayName = "counts",
      positionType = NULL,
      positionColData = NULL
    )

### Arguments

`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.

### Value

A scHOT object

### Examples

    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)

[Package scHOT version 1.4.0 Index]