get_edge_list {BioNERO} | R Documentation

## 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`,`corPvalueStudent` `fit_power_law`

`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)

[Package BioNERO version 1.0.4 Index]