GENIE3OOB: GENIE3OOB

In OceaneCsn/DIANE: DIANE

GENIE3OOB

Description

GENIE3OOB Infers a gene regulatory network (in the form of a pvalues-filled adjacency matrix) from expression data, using ensembles of regression trees.

Usage

GENIE3OOB(
  exprMatrix,
  regulators = NULL,
  targets = NULL,
  nTrees = 1000,
  nCores = 1,
  verbose = FALSE
)

Arguments

exprMatrix	Expression matrix (genes x samples). Every row is a gene, every column is a sample.
regulators	Subset of genes used as candidate regulators. Must be either a vector of indices, e.g. c(1,5,6,7), or a vector of gene names, e.g. c("at_12377", "at_10912"). The default value NULL means that all the genes are used as candidate regulators.
targets	Subset of genes to which potential regulators will be calculated. Must be either a vector of indices, e.g. c(1,5,6,7), or a vector of gene names, e.g. c("at_12377", "at_10912"). If NULL (default), regulators will be calculated for all genes in the input matrix.
nTrees	Number of trees in an ensemble for each target gene. Default: 1000.
nCores	Number of cores to use for parallel computing. Default: 1.
verbose	If set to TRUE, a feedback on the progress of the calculations is given. Default: TRUE

Value

matrix containing oob importances for all TF-gene pairs

OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.