Niche_DE — niche_DE • nicheDE

This function performs niche-DE

Usage

niche_DE(
  object,
  num_cores,
  outfile,
  C = 150,
  M = 10,
  gamma = 0.8,
  print = T,
  Int = T,
  batch = T,
  self_EN = F,
  G = 1
)

object: A niche-DE object
num_cores: The number of cores to parallelize on
outfile: The file path to write progress on
C: Minimum total expression of a gene needed for the model to run. Default value is 150.
M: Minimum number of spots containing the index cell type with the niche cell type in its effective niche for (index,niche) niche patterns to be investigated. Default value is 10.
gamma: Percentile a gene needs to be with respect to expression in the index cell type in order for the model to investigate niche patterns for that gene in the index cell. Default value is 0.8 (80th percentile)
print: Logical if function should print progress report (kernel, gene #)
Int: Logical if data is count data. If True, negative binomial regression is performed. Otherwise linear regression with a gene specific variance is applied. Default is True.
batch: Logical if an indicator should be included for each batch in the regression. Default is True.
G: Number of gigabytes each core should hold. If the counts matrix is bigger than G, it is split into multiple chunks such that the size of each chunk is less than G gigabytes.
Self_EN: Should niche interactions between the same cell types be considered. Default is False.

A niche-DE object with niche-DE analysis performed