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()

Value

Data frame with edge list for the input genes.

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.

Author

Fabricio Almeida-Silva

Examples

data(filt.se)
gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson")
#> ..connectivity..
#> ..matrix multiplication (system BLAS)..
#> ..normalization..
#> ..done.
genes <- rownames(filt.se)[1:50]
edges <- get_edge_list(gcn, genes=genes, filter = FALSE)