scHOT_buildFromSCE: scHOT_buildFromSCE

In shazanfar/scHOT: single-cell higher order testing

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)

shazanfar/scHOT documentation built on June 29, 2023, 5:29 p.m.