LoadLR | R Documentation |
Load ligand-receptor database
LoadLR(
species = "human",
database = "OmniPath",
ligands = NULL,
recepts = NULL,
lit_support = 7
)
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. |
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.
Turei, et al. Molecular Systems Biology (2021); Raredon, et al. bioRxiv (2021)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.