LoadLR: Load ligand-receptor database

In BlishLab/scriabin: Single-cell resolved interaction analysis through binning

Load ligand-receptor database

Description

Load ligand-receptor database

Usage

LoadLR(
  species = "human",
  database = "OmniPath",
  ligands = NULL,
  recepts = NULL,
  lit_support = 7
)

Arguments

species	character. Name of species from which to load ligand-receptor databases. One of: "human", "mouse", "rat". Default: "human"
database	Name of ligand-receptor database to use. Default: "OmniPath" When species is "human", one of: OmniPath, CellChatDB, CellPhoneDB, Ramilowski2015, Baccin2019, LRdb, Kirouac2010, ICELLNET, iTALK, EMBRACE, HPMR, Guide2Pharma, connectomeDB2020, talklr, CellTalkDB When species is "mouse" or "rat", only "OmniPath" is supported. To pass a custom ligand-receptor database to this function, set database = "custom"
ligands	Character vector of custom ligands to use for interaction graph generation. Ignored unless database = "custom" When ligands is supplied, recepts must also be supplied and equidimensional.
recepts	Character vector of custom receptors to use for interaction graph generation. Ignored unless database = "custom" When recepts is supplied, ligands must also be supplied and equidimensional.
lit_support	Numeric. Only entries with curation_effort (number of unique database - citation pairs per interaction) greater than or equal to this value are retained. Default 7.

Value

Returns a dataframe containing gene symbols for ligand and receptor pairs. Column "pair" contains underscore-separated ligand-receptor pairs. Ligand and receptor gene names are stored in "source_genesymbol" and "target_genesymbol", respectively.

References

Turei, et al. Molecular Systems Biology (2021); Raredon, et al. bioRxiv (2021)

BlishLab/scriabin documentation built on July 5, 2023, 1:14 a.m.