calculatePathlength: Calculate pathlength from binary interactions

In CCprofiler/CCprofiler: Complex feature detection using SEC protein chromatograms.

Description

Calculate shortest paths between all members of a binary interaction network. This function creates a table that contains all possible combinations of 2 from all input proteins (binomial coefficient (length(proteins) over 2)).

Usage

calculatePathlength(binaryInteractionTable)

Arguments

binaryInteractionTable

data.table with binary interactions between "a" and "b" as returned from generateBinaryNetwork()

Value

data.table with three columns containing all possible combinations of proteins:

• x,y: Protein ids of the input proteins (all possible combinations)

• dist: distance (shortest path between interactors) as determined by the input binary interaction table

Examples

## Load example data
complexHypotheses <- exampleComplexHypotheses

## Generate the binary network
binaryInteractions <- generateBinaryNetwork(complex_hypotheses = complexHypotheses)

## Calculate the path lengths
shortestPaths <- calculatePathlength(binaryInteractions)

CCprofiler/CCprofiler documentation built on May 19, 2021, 7:40 p.m.