assess_synnet_list: Assess list of synteny networks as in 'assess_synnet'
In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

assess_synnet_list

R Documentation

Assess list of synteny networks as in `assess_synnet`

Description

Assess list of synteny networks as in assess_synnet

Usage

assess_synnet_list(synnet_list = NULL, cc_type = "average")

Arguments

`synnet_list`	A list of networks, each network being an edge list as 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'.
Network: Character of network name.

Examples

set.seed(123)
data(synnet)
net1 <- synnet
net2 <- synnet[-sample(1:10000, 500), ]
net3 <- synnet[-sample(1:10000, 1000), ]
synnet_list <- list(net1 = net1, net2 = net2, net3 = net3)
assess_synnet_list(synnet_list)

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