Skip to contents

Getniche genes for the given index and niche cell types at the desired test.level

get_niche_DE_genes.Rd

This function returns genes that show niche patterns at the desired test.level

Usage

get_niche_DE_genes(
  object,
  test.level,
  index,
  niche,
  positive = T,
  alpha = 0.05
)

Arguments

object

A niche-DE object

test.level

At which test.level to return genes (gene level ("G"), cell type level("CT"), interaction level("I"))

index

The index cell type

niche

The niche cell type

positive

Logica indicating whether to return upregulated/positive niche-DE genes(True) or downregulated/negative niche-DE genes(False). Default value is True.

alpha

The level at which to perform the Benjamini Hochberg correction. Default value = 0.05

Value

A vector of genes that are niche significant at the desired FDR, test.level, index cell type, and niche cell type