edgesToHubNetworks {ClassifyR} | R Documentation

## Convert a Two-column Matrix or Data Frame into a Hub Node List

### Description

Interactions between pairs of features (typically a protein-protein interaction, commonly abbreviated as PPI, database) are restructured into a named list. The name of the each element of the list is a feature and the element contains all features which have an interaction with it.

### Usage

      edgesToHubNetworks(edges, minCardinality = 5)

### Arguments

`edges` | A two-column `matrix` or `data.frame` for which each row specifies a known interaction betwen two interactors. If feature X appears in the first column and feature Y appears in the second, there is no need for feature Y to appear in the first column and feature X in the second.
`minCardinality` | An integer specifying the minimum number of features to be associated with a hub feature for it to be present in the result.

### Value

An object of type `FeatureSetCollection`.

### Author(s)

Dario Strbenac

### References

VAN: an R package for identifying biologically perturbed networks via differential variability analysis, Vivek Jayaswal, Sarah-Jane Schramm, Graham J Mann, Marc R Wilkins and Yee Hwa Yang, 2010, BMC Research Notes, Volume 6 Article 430, https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-6-430.

### Examples

      interactor <- c("MITF", "MITF", "MITF", "MITF", "MITF", "MITF",
                      "KRAS", "KRAS", "KRAS", "KRAS", "KRAS", "KRAS",
                      "PD-1")
      otherInteractor <- c("HINT1", "LEF1", "PSMD14", "PIAS3", "UBE2I", "PATZ1",
                           "ARAF", "CALM1", "CALM2", "CALM3", "RAF1", "HNRNPC",
                           "PD-L1")
      edges <- data.frame(interactor, otherInteractor, stringsAsFactors = FALSE)

      edgesToHubNetworks(edges, minCardinality = 4)

[Package ClassifyR version 2.4.4 Index]