grn_combined {BioNERO} | R Documentation |
Infer gene regulatory network with multiple algorithms and combine results in a list
grn_combined( exp, regulators = NULL, eps = 0.1, estimator_aracne = "spearman", estimator_clr = "pearson", remove_zero = TRUE, ... )
exp |
A gene expression data frame with genes in row names and samples in column names or a 'SummarizedExperiment' object. |
regulators |
A character vector of regulators (e.g., transcription factors or miRNAs). All regulators must be included in 'exp'. |
eps |
Numeric value indicating the threshold used when removing an edge: for each triplet of nodes (i,j,k), the weakest edge, say (ij), is removed if its weight is below min(ik),(jk) - eps. Default: 0.1. |
estimator_aracne |
Entropy estimator to be used in ARACNE inference. One of "mi.empirical", "mi.mm", "mi.shrink", "mi.sg", "pearson", "spearman", or "kendall". Default: "spearman". |
estimator_clr |
Entropy estimator to be used in CLR inference. One of "mi.empirical", "mi.mm", "mi.shrink", "mi.sg", "pearson", "spearman", or "kendall". Default: "pearson". |
remove_zero |
Logical indicating whether to remove edges whose weight is exactly zero. Zero values indicate edges that were removed by ARACNE. Default: TRUE. |
... |
Additional arguments passed to 'GENIE3::GENIE3()'. |
A list of data frames representing edge lists. Each list element is an edge list for a specific method.
data(filt.se) tfs <- sample(rownames(filt.se), size=50, replace=FALSE) grn_list <- grn_combined(filt.se, regulators=tfs, nTrees=2)