Perform Niche-LR (Ligand receptor analysis) on spot level data
niche_LR_spot.RdThis function returns ligands and receptors inferred to be expressed by the given cell types
Usage
niche_LR_spot(
object,
ligand_cell,
receptor_cell,
ligand_target_matrix,
lr_mat,
K = 25,
M = 50,
alpha = 0.05,
truncation_value = 3
)Arguments
- object
A niche-DE object
- ligand_cell
The cell type that expresses the ligand
- receptor_cell
The cell type that expresses the receptor
- ligand_target_matrix
A matrix that measures the association between ligands and their downstream target genes. Should be target genes by ligands
- lr_mat
A matrix that matches ligands with their corresponding receptors. This matrix should have two columns. The first will be ligands and the second will be the corresponding receptors
- K
The number of downstream target genes to use when calculating the ligand potential score. Default value is 25.
- M
The maximum number of ligands that can pass initial filtering. Default value is 50.
- alpha
The level at which to perform the Benjamini Hochberg correction. Default value is 0.05.
- truncation_value
The value at which to truncate T statistics. Default value is 3.