curated_ligand_receptor_interactions: Curated ligand-receptor interactions

In saezlab/OmnipathR: OmniPath web service client and more

Curated ligand-receptor interactions

Description

The OmniPath intercell database annotates individual proteins and complexes, and we combine these annotations with network interactions on the client side, using import_intercell_network. The architecture of this database is complex, aiming to cover a broad range of knowledge on various levels of details and confidence. We can use the intercell_consensus_filter and filter_intercell_network functions for automated, data driven quality filtering, in order to enrich the cell-cell communication network in higher confidence interactions. However, for many users, a simple combination of the most established, expert curated ligand-receptor resources, provided by this function, fits better their purpose.

Usage

curated_ligand_receptor_interactions(
  curated_resources = c("Guide2Pharma", "HPMR", "ICELLNET", "Kirouac2010", "CellTalkDB",
    "CellChatDB", "connectomeDB2020"),
  cellphonedb = TRUE,
  cellinker = TRUE,
  talklr = TRUE,
  signalink = TRUE,
  ...
)

Arguments

curated_resources	Character vector of the resource names which are considered to be expert curated. You can include any post-translational network resource here, but if you include non ligand-receptor or non curated resources, the result will not fulfill the original intention of this function.
cellphonedb	Logical: include the curated interactions from CellPhoneDB (not the whole CellPhoneDB but a subset of it).
cellinker	Logical: include the curated interactions from Cellinker (not the whole Cellinker but a subset of it).
talklr	Logical: include the curated interactions from talklr (not the whole talklr but a subset of it).
signalink	Logical: include the ligand-receptor interactions from SignaLink. These are all expert curated.
...	Passed to import_post_translational_interactions: further parameters for the interaction data. Should not contain 'resources' argument as that would interfere with the downstream calls.

Details

Some resources are a mixture of curated and bulk imported interactions, and sometimes it's not trivial to separate these, we take care of these here. This function does not use the intercell database of OmniPath, but retrieves and filters a handful of network resources. The returned data frame has the layout of interactions (network) data frames, and the source and target partners implicitly correspond to ligand and receptor. The data frame shows all resources and references for all interactions, but each interaction is supported by at least one ligand-receptor resource which is supposed to based on expert curation in a ligand-receptor context.

Value

A data frame similar to interactions (network) data frames, the source and target partners being ligand and receptor, respectively.

See Also

• import_intercell_network

• filter_intercell_network

• annotated_network

• import_post_translational_interactions

• import_ligrecextra_interactions

• curated_ligrec_stats

Examples

lr <- curated_ligand_receptor_interactions()
lr

saezlab/OmnipathR documentation built on May 3, 2024, 5:32 a.m.