Skip to contents

Assess synteny network based on graph properties

Usage

assess_synnet(synnet = NULL, cc_type = "average")

Arguments

synnet

Edge list for the synteny network in a 2-column data frame, with columns 1 and 2 representing names of loci in anchor 1 and anchor 2, respectively.

cc_type

Type of clustering coefficient to be calculated. One of 'global' or 'average'. Default: 'average'.

Value

A data frame with the following variables:

CC

Numeric representing clustering coefficient.

Node_count

Numeric representing number of nodes in the network.

Rsquared

Numeric indicating the coefficient of determination for the scale-free topology fit.

Score

Numeric representing network score, which is the product of 'CC' and 'Node_number'.

Details

Network score is the product of the network's clustering coefficient, node count, and R squared for the scale-free topology fit.

Examples

data(synnet)
assess_synnet(synnet)
#>         CC Node_count  Rsquared    Score
#> 1 0.877912     149144 0.6806854 89125.76