get_edge_list: Get edge list from an adjacency matrix for a group of genes

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

Get edge list from an adjacency matrix for a group of genes

Description

Get edge list from an adjacency matrix for a group of genes

Usage

get_edge_list(
  net,
  genes = NULL,
  module = NULL,
  filter = FALSE,
  method = "optimalSFT",
  r_optimal_test = seq(0.4, 0.9, by = 0.1),
  Zcutoff = 1.96,
  pvalue_cutoff = 0.05,
  rcutoff = 0.7,
  nSamples = NULL,
  check_SFT = FALSE,
  bp_param = BiocParallel::SerialParam()
)

Arguments

net	List object returned by exp2gcn.
genes	Character vector containing a subset of genes from which edges will be extracted. It can be ignored if the user wants to extract an edge list for a given module instead of individual genes.
module	Character with module name from which edges will be extracted. To include 2 or more modules, input the names in a character vector.
filter	Logical indicating whether to filter the edge list or not.
method	Method to filter spurious correlations. One of "Zscore", "optimalSFT", "pvalue" or "min_cor". See details for more information on the methods. Default: 'optimalSFT'
r_optimal_test	Numeric vector with the correlation thresholds to be tested for optimal scale-free topology fit. Only valid if method equals "optimalSFT". Default: seq(0.4, 0.9, by = 0.1)
Zcutoff	Minimum Z-score threshold. Only valid if method equals "Zscore". Default: 1.96
pvalue_cutoff	Maximum P-value threshold. Only valid if method equals "pvalue". Default: 0.05
rcutoff	Minimum correlation threshold. Only valid if method equals "min_cor". Default: 0.7
nSamples	Number of samples in the data set from which the correlation matrix was calculated. Only required if method equals "pvalue".
check_SFT	Logical indicating whether to test if the resulting network is close to a scale-free topology or not. Default: FALSE.
bp_param	BiocParallel back-end to be used. Default: BiocParallel::SerialParam()

Details

The default method ("optimalSFT") will create several different edge lists by filtering the original correlation matrix by the thresholds specified in r_optimal_test. Then, it will calculate a scale-free topology fit index for each of the possible networks and return the network that best fits the scale-free topology. The method "Zscore" will apply a Fisher Z-transformation for the correlation coefficients and remove the Z-scores below the threshold specified in Zcutoff. The method "pvalue" will calculate Student asymptotic p-value for the correlations and remove correlations whose p-values are above the threshold specified in pvalue_cutoff. The method "min_cor" will remove correlations below the minimum correlation threshold specified in rcutoff.

Value

Data frame with edge list for the input genes.

Author(s)

Fabricio Almeida-Silva

See Also

scaleFreeFitIndex

SFT_fit

exp2gcn.

Examples

data(filt.se)
gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson")
genes <- rownames(filt.se)[1:50]
edges <- get_edge_list(gcn, genes=genes, filter = FALSE)

almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.