Function to Generate OmniPath versions

generate_omni(remove_complexes = TRUE, simplify = TRUE, ...)

Arguments

remove_complexes

whether to remove complexes

simplify

whether to simplify according to the mandatory columns needed by different methods in `liana`

...

Arguments passed on to OmnipathR::filter_intercell_network

network: An intercell network data frame, as provided by import_intercell_network, without simplify.
transmitter_topology: Character vector: topologies allowed for the entities in transmitter role. Abbreviations allowed: "sec", "pmtm" and "pmp".
receiver_topology: Same as transmitter_topology for the entities in the receiver role.
min_curation_effort: Numeric: a minimum value of curation effort (resource-reference pairs) for network interactions. Use zero to disable filtering.
min_resources: Numeric: minimum number of resources for interactions. The value 1 means no filtering.
min_references: Numeric: minimum number of references for interactions. Use zero to disable filtering.
min_provenances: Numeric: minimum number of provenances (either resources or references) for interactions. Use zero or one to disable filtering.
consensus_percentile: Numeric: percentile threshold for the consensus score of generic categories in intercell annotations. 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 consensus_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.
ligand_receptor: Logical. If TRUE, only ligand and receptor annotations will be used instead of the more generic transmitter and receiver categories.
unique_pairs: Logical: instead of having separate rows for each pair of annotations, drop the annotations and reduce the data frame to unique interacting pairs. See unique_intercell_network for details.
omnipath: Logical: shortcut to include the omnipath dataset in the interactions query.
ligrecextra: Logical: shortcut to include the ligrecextra dataset in the interactions query.
kinaseextra: Logical: shortcut to include the kinaseextra dataset in the interactions query.
pathwayextra: Logical: shortcut to include the pathwayextra dataset in the interactions query.

Value

An OmniPath resource