View source: R/application_prediction.R
bootstrap_ligand_activity_analysis | R Documentation |
bootstrap_ligand_activity_analysis
Randomly sample a gene set from all expressed genes in the receiver cell type, then perform ligand activity analysis on this gene set. This 'null gene set' has equal length to the gene set of interest.
bootstrap_ligand_activity_analysis(expressed_genes_receiver, geneset_oi, background_expressed_genes, ligand_target_matrix, potential_ligands, n_iter = 10, n_cores = 1, parallel_func = "mclapply")
expressed_genes_receiver |
Genes expressed in the receiver cell type |
geneset_oi |
Character vector of the gene symbols of genes of which the expression is potentially affected by ligands from the interacting cell. |
background_expressed_genes |
Character vector of gene symbols of the background, non-affected, genes (can contain the symbols of the affected genes as well). |
ligand_target_matrix |
The NicheNet ligand-target matrix denoting regulatory potential scores between ligands and targets (ligands in columns). |
potential_ligands |
Character vector giving the gene symbols of the potentially active ligands you want to define ligand activities for. |
n_iter |
Number of iterations to perform (Default: 10) |
n_cores |
Number of cores to use for parallelization (Default: 1) |
parallel_func |
Parallelization function to use from "mclapply", "pbmclapply", or "parLapply" (Default: "mclapply") |
List of n_iter elements, each element containing the output of predict_ligand_activities for a random gene set
## Not run:
permutations <- bootstrap_ligand_activity_analysis(expressed_genes_receiver, geneset_oi, background_expressed_genes,
ligand_target_matrix, potential_ligands, n_iter = 10, n_cores = 1, parallel_func = "mclapply")
## End(Not run)
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