Skip to contents

Score the networks composed of a ranked list of genes

score_networks.Rd

The networks are scored by:

  • modularity;

  • network components;

  • omega z-score peaks;

  • presence of linkers.

Usage

score_networks(
  g_CC_LCC = NULL,
  X0 = NULL,
  X0_column = 1,
  NRsummary = NULL,
  commMethods = "fastgreedy",
  BPPARAM = NULL
)

Arguments

g_CC_LCC

list of CC and LCC as produced by means of calc_CC_LCC()

X0

the X0 matrix

X0_column

the column of X0 that will be considered

NRsummary

NRsummary element of the output of function NR()

commMethods

community method(s) that will be considered

BPPARAM

optional BBPARAM

Value

A data frame with the following quantities for CC and LCC:

  • X0_: sum of the X0 values in the network divided by the sum of the n genes with the highest X0 values, where n network size (CC or LCC);

  • linkers: fraction of linkers, that is, genes with X0(i) equal to 0;

  • omega: NR omega value;

  • z: omega z-score;

  • p_val: omega p_val;

  • n_V_: number of vertices;

  • n_E_: number of links;

  • a_: algorithm used to find the communities;

  • Q_: modularity;

  • n_comm_: number of communities.