Quality filter for intercell annotationsSource:
Quality filter for intercell annotations
A data frame with intercell annotations, as provided by
Numeric: a percentile cut off for the consensus score of composite 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
NULLno 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.
Numeric: similar to
percentilefor major localizations. For example, with a value of 50, the secreted, plasma membrane transmembrane or peripheral attributes will be
TRUEonly where at least 50 percent of the resources support these.
Character vector: list of allowed topologies, possible values are *"secreted"*, *"plasma_membrane_peripheral"* and *"plasma_membrane_transmembrane"*.
intercell <- import_omnipath_intercell(parent = c('ligand', 'receptor')) nrow(intercell) #>  60805 #  50174 intercell_q50 <- intercell_consensus_filter(intercell, 50) nrow(intercell_q50) #>  58423 #  42863