spatial_variable_genes: Find spatial variable genes

In Czh3/iSpatial: infer transcriptome-wide spatial expression via integration of scRNA and spRNA

Find spatial variable genes

Description

Bin the images into small chunks. For each gene, detected the numbers of expression cells in each chunk, comparing the distribution with random.

Usage

spatial_variable_genes(
  spRNA.obj,
  spRNA.assay = "enhanced",
  scRNA.obj = NULL,
  scRNA.assay = "RNA",
  test.use = "wilcox",
  bin = 20,
  n.core = 1
)

Arguments

spRNA.obj	spatial transcriptome seurat object
spRNA.assay	spatial transcriptome assay
scRNA.obj	scRNA-seq seurat object
scRNA.assay	scRNA-seq seurat assay
test.use	which test to use. Available options are: "ks": Kolmogorov-Smirnov Tests "wilcox": Wilcoxon Rank Sum and Signed Rank Tests
bin	number of bins used to segregate the image
n.core	number of CPU cores used

Value

return a matrix wtih spatial variable genes

Czh3/iSpatial documentation built on Sept. 15, 2022, 10:32 p.m.