CreateNicheDEObject

This function creates a niche-DE object

Usage

CreateNicheDEObject(
  counts_mat,
  coordinate_mat,
  library_mat,
  deconv_mat,
  sigma,
  Int = T
)

Arguments

counts_mat

Counts matrix. Dimension should be cells/spots by genes

coordinate_mat

Coordinate matrix. It will be scaled such that the median nearest neighbor distance is 100.

library_mat

Matrix indicating average expression profile for each cell type in the sample

deconv_mat

Deconvolution or cell type assignment matrix of data

sigma

List of kernel bandwidths to use in calculating the effective niche

Int

Boolean of if counts data supplied is integer. Default is true. When performing niche-DE, Negative binomial regression is performed if True. Linear regression with a gene specific variance is performed if False.

Value

A niche-DE object