Symmetrizes each square matrix in a list by ensuring entries (i, j) and (j, i) are identical, using a specified combination function.
Arguments
- matrix_list
A list of square numeric matrices to symmetrize.
- weight_function
Character string or function. Method to combine entries (i, j) and (j, i). Options include
"mean","max","min", or a user-defined function.- nCores
Integer. Number of CPU cores to use for parallel processing. Defaults to the number of available workers in the current BiocParallel backend.
Value
A list of symmetric matrices, where for each matrix \(A[i, j] = A[j, i]\) for all \(i \neq j\).
Details
For each pair of off-diagonal elements (i, j) and (j, i):
If one value is zero, the non-zero value is used.
If both are non-zero, they are combined using the specified
weight_function.
Diagonal entries are preserved as-is and not modified.
Parallelization is managed via BiocParallel for improved performance.
Examples
data("count_matrices")
networks <- infer_networks(
count_matrices_list = count_matrices,
method = "GENIE3",
nCores = 1
)
head(networks[[1]])
#> regulatoryGene targetGene weight
#> 1 HLA-A CD74 0.1928279
#> 2 ARPC2 ARPC3 0.1924564
#> 3 ARPC3 ARPC2 0.1664078
#> 4 CD3E JUN 0.1549951
#> 5 CD3E CD3D 0.1495645
#> 6 HLA-E FOS 0.1492515
wadj_list <- generate_adjacency(networks)
swadj_list <- symmetrize(wadj_list, weight_function = "mean")