grn_combined: Infer gene regulatory network with multiple algorithms and...

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

Infer gene regulatory network with multiple algorithms and combine results in a list

Description

Infer gene regulatory network with multiple algorithms and combine results in a list

Usage

grn_combined(
  exp,
  regulators = NULL,
  eps = 0.1,
  estimator_aracne = "spearman",
  estimator_clr = "pearson",
  remove_zero = TRUE,
  ...
)

Arguments

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()'.

Value

A list of data frames representing edge lists. Each list element is an edge list for a specific method.

Examples

data(filt.se)
tfs <- sample(rownames(filt.se), size=50, replace=FALSE)
grn_list <- grn_combined(filt.se, regulators=tfs, nTrees=2)

almeidasilvaf/BioNERO documentation built on March 25, 2024, 9:14 p.m.