assess_synnet: Assess synteny network based on graph properties

In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

Assess synteny network based on graph properties

Description

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'.

Details

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

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'.

Examples

data(synnet)
assess_synnet(synnet)

almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.