This function calculates the effective niche of a niche-DE object
Usage
CalculateEffectiveNicheLargeScale(
object,
batch_size = 1000,
cutoff = 0.05,
standardize = TRUE
)
Arguments
- object
A niche-DE object
- batch_size
Number of cells to calculate the effective niche for at a time
- cutoff
Minimum kernel similarity. Similarities below this value get truncated to 0
- standardize
A logical indicator for if the effective niche should be z-normalized by column
Value
A niche-DE object the effective niche calculated.
The effective niche is a list with each entry corresponding to a kernel bandwidth