omnipath_partners: Retrieves intercellular communication partners (transmitters...

In saezlab/ligrec_decoupler: LIANA: a LIgand-receptor ANalysis frAmework

Retrieves intercellular communication partners (transmitters or receivers) from OmniPath

Description

Retrieves intercellular communication partners (transmitters or receivers) from OmniPath

Usage

omnipath_partners(side, ...)

Arguments

side

'ligand' (trans), 'receptor' (rec) or 'both' (both short or long notation can be used)

...

Arguments passed on to OmnipathR::import_omnipath_intercell categories vector containing the categories to be retrieved. All the genes belonging to those categories will be returned. For further information about the categories see codeget_intercell_categories. resources limit the query to certain resources; see the available resources by get_intercell_resources. parent vector containing the parent classes to be retrieved. All the genes belonging to those classes will be returned. For furter information about the main classes see get_intercell_categories. scope either 'specific' or 'generic' aspect either 'locational' or 'functional' source either 'resource_specific' or 'composite' transmitter logical, include only transmitters i.e. proteins delivering signal from a cell to its environment. receiver logical, include only receivers i.e. proteins delivering signal to the cell from its environment. secreted logical, include only secreted proteins plasma_membrane_peripheral logical, include only plasma membrane peripheral membrane proteins. plasma_membrane_transmembrane logical, include only plasma membrane transmembrane proteins. proteins limit the query to certain proteins topology topology categories: one or more of 'secreted' (sec), 'plasma_membrane_peripheral' (pmp), 'plasma_membrane_transmembrane' (pmtm) (both short or long notation can be used). causality 'transmitter' (trans), 'receiver' (rec) or 'both' (both short or long notation can be used). consensus_percentile Numeric: a percentile cut off for the consensus score of generic categories. The consensus score is the number of resources supporting the classification of an entity into a category based on combined information of many resources. Here you can apply a cut-off, keeping only the annotations supported by a higher number of resources than a certain percentile of each category. If NULL no filtering will be performed. The value is either in the 0-1 range, or will be divided by 100 if greater than 1. The percentiles will be calculated against the generic composite categories and then will be applied to their resource specific annotations and specific child categories. loc_consensus_percentile Numeric: similar to codeconsensus_percentile for major localizations. For example, with a value of 50, the secreted, plasma membrane transmembrane or peripheral attributes will be true only where at least 50 percent of the resources support these.

saezlab/ligrec_decoupler documentation built on Aug. 10, 2024, 8:56 a.m.