SpaGene_sparse: Identify spatially variable genes for extremely sparse data

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

Identify spatially variable genes for extremely sparse data

Description

Identify spatial variable genes based on spatial connectness of spots/cells with high expression. For genes with different sparsity level, the function adjusts the neighborhood search region automatically.

Usage

SpaGene_sparse(
  expr,
  location,
  normalize = TRUE,
  maxN = floor(0.1 * dim(location)[1]),
  minN = 50,
  perm = 500,
  sizefactor = 10000,
  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
normalize	whether to normalize the data (default: TRUE)
maxN	the maximum number of spots/cells considered high expression (default: 10 percent of the total spots/cells)
minN	the minimum number of spots/cells considered high expression (default: 50. genes with less than 50 cells/spots expressed are excluded)
perm	the number of random permutations (default: 500)
sizefactor	the size factor for normalization (default:10000)
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 can be a numeric vector of length 2*knn+1 (default:NULL)

Value

a list containing results of each gene (spagene_res) and normalized gene expression matrix (normexp)

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