Assess synteny network based on graph properties — assess_synnet • cogeqc

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