thinning_scale_free: Subset a coexpression network to maximise free scale fit

In ne1s0n/MTGOsc: MTGO analysis applied to Single Cell data

Subset a coexpression network to maximise free scale fit

Description

This function removes edges from the passed network so that the resulting subnetwork is maximally scale free. First, for each value in thresholds argument, a subnetwork is created. Each subnetwork is obtained from the original x removing all edges smaller, in absolute value, than the corresponding threshold. Then each subnetwork is fitted a power law, and the one whose gamma is closest to target.gamma is selected.

Usage

thinning_scale_free(x, thresholds = seq(from = 0.1, to = 0.9, by = 0.1),
  target.gamma = 2, verbose = TRUE)

Arguments

x	a coexpression network, as returned by write.coexpressionMatrix
thresholds	numeric array of thresholds to be considered
target.gamma	for biological networks target gamma is somewhere between 2 and 3
verbose	should extra informations be printed?

Value

a smaller version of the original matrix

ne1s0n/MTGOsc documentation built on April 20, 2022, 9:35 p.m.