SpaGene_CT: Identify spatially variable genes within the same cell type

In liuqivandy/SpaGene: Identify spatially localized genes and colocalized gene pairs

Identify spatially variable genes within the same cell type

Description

Identify spatial variable genes within the same cell type

Usage

SpaGene_CT(
  expr,
  location,
  CellType,
  normalize = T,
  top = 0.2,
  knn = 8,
  minN = 0,
  perm = 500,
  weight = NULL
)

Arguments

expr	gene expression matrix, the row is the gene and the column is the spot/cell
location	location matrix, the row number of location should match the column number of expr
CellType	the cell type, the length should match the column number of locations
normalize	whether to normalize the data (default: TRUE)
top	the maximum ratio of spots/cells in the same cell type considered high expression (default: 20 percent of the spots/cells within a cell type, 10 is used if top is less than 10)
knn	the number of nearest neighbours to search (default: 8)
minN	the minimum number of spots/cells (default: 0. genes with less than or equal to minN cells/spots expressed are excluded)
perm	the number of random permutations (default: 500)
weight	weights assigned to degree. If NULL, equal weight, wi=1, i is the degree, i=0,1,...2*knn; if "linear", wi=0.5+0.5*i/(2*knn); or weight is a numeric vector of length 2*knn+1 (default:NULL)

Value

a data frame containing results of each gene in each cell type

liuqivandy/SpaGene documentation built on July 1, 2023, 6:44 a.m.