SpaGene: Identify spatially variable genes

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

Identify spatially variable genes

Description

Identify spatial variable genes based on spatial connectness of spots with high expression compared to random permutation

Usage

SpaGene(
  expr,
  location,
  normalize = T,
  topn = floor(0.2 * dim(location)[1]),
  knn = 8,
  perm = 500,
  minN = 0,
  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)
topn	the ratio of spots/cells considered high expression (default: 20 percent of the total spots/cells)
knn	the number of nearest neighbours to search (default: 8)
perm	the number of random permutations (default: 500)
minN	the minimum number of spots/cells with gene expression. Genes expressed equal to or less than minN spots/cells are excluded (default:0)
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 is 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.