corTools (version 1.0)

edgecount: Edge counter

Description

Counts the number of relationships any given trait makes, to find central hubs of traits with many relationships. Built with Cytoscape in mind, where the function counts edges and returns the names of nodes with the most edges.

Usage

edgecount(dat, col1, col2)

Arguments

dat

Dataframe name, containing the traits entered as columns.

col1

First column of trait names

col2

Second column of trait names

Value

Details

This function helps identify key nodes in an interaction network by identifying the nodes with the most interactions through an incremented counter. This function will edit out redundant interactions and return only a unique list of traits- this means that interactions that are repeated will not be redundantly counted, and each trait will only be listed once in the returned frequency table.

References

http://www.cytoscape.org/ Krouk G, Mirowski P, LeCun Y, Shasha DE, Coruzzi GM (2010) Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol 11(12):R123.

Examples

# Create a sample dataset
Interaction1 <- c("L1", "L2", "L3", "L4", "L19", "R7", "L2")
Interaction2 <- c("L1", "L9", "R1", "R2", "R7", "L4", "R10")
dat <- as.data.frame(cbind(Interaction1, Interaction2))

edgecount(dat, Interaction1, Interaction2)
# dat denotes the name of the data frame
# Interaction1 and Interaction2 denote the column names of the dataframe that contain the
# traits whose interactions you want to count
# function returns a list of unique traits and their frequency of appearance
# Example: L1 only appears once, so it is L1   1
# L4 appears twice, so it is L4   2