LRscore: Score ligand-receptor interactions
In Jasonxu0109/PlantPhoneDB: PlantPhoneDB in R

LRscore

R Documentation

Score ligand-receptor interactions

Score ligand-receptor interactions

LRscore(
  expr,
  LRdb,
  cluster = NULL,
  min.pct = 0.1,
  method = "LRscore",
  iterations = 100,
  seed = 123,
  ...
)

`expr`	A data frame or matrix of n rows (genes) and m columns (cells) normalized by SCTransform().
`LRdb`	A dataset with ligand-receptor pairs, such as LR_pair_ath.RDa.
`cluster`	A numeric vector of length m.
`min.pct`	Only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Default is 0.1.
`method`	Denotes which test to use. Available options are: "LRscore" : Score ligand-receptor interactions using a new regularized product score (Cabello-Aguilar et al., Nucleic Acids Research, 2020). "WeightProduct" : Score ligand-receptor interactions using an edge-score model (Altmann et al., Nature, 2020) "Average" : Score ligand-receptor interactions using mean ligand expression level + mean receptor expression level (Efremova et al., Nature Protocols, 2020). "Product" : Score ligand-receptor interactions using mean ligand expression level × mean receptor expression level.
`iterations`	Ligand-receptor interactions scores were calculated using a permutation test by randomly shuffling the cluster labels if method set Average or Product. Default is 100.
`seed`	Random seed. Default is 123.
`...`