run_mdt: Multivariate Decision Trees (MDT)

In saezlab/decoupleR: decoupleR: Ensemble of computational methods to infer biological activities from omics data

Multivariate Decision Trees (MDT)

Description

Calculates regulatory activities using MDT.

Usage

run_mdt(
  mat,
  network,
  .source = source,
  .target = target,
  .mor = mor,
  .likelihood = likelihood,
  sparse = FALSE,
  center = FALSE,
  na.rm = FALSE,
  trees = 10,
  min_n = 20,
  nproc = availableCores(),
  seed = 42,
  minsize = 5
)

Arguments

mat	Matrix to evaluate (e.g. expression matrix). Target nodes in rows and conditions in columns. rownames(mat) must have at least one intersection with the elements in network .target column.
network	Tibble or dataframe with edges and it's associated metadata.
.source	Column with source nodes.
.target	Column with target nodes.
.mor	Column with edge mode of regulation (i.e. mor).
.likelihood	Deprecated argument. Now it will always be set to 1.
sparse	Deprecated parameter.
center	Logical value indicating if mat must be centered by base::rowMeans().
na.rm	Should missing values (including NaN) be omitted from the calculations of base::rowMeans()?
trees	An integer for the number of trees contained in the ensemble.
min_n	An integer for the minimum number of data points in a node that are required for the node to be split further.
nproc	Number of cores to use for computation.
seed	A single value, interpreted as an integer, or NULL for random number generation.
minsize	Integer indicating the minimum number of targets per source.

Details

MDT fits a multivariate regression random forest for each sample, where the observed molecular readouts in mat are the response variable and the regulator weights in net are the covariates. Target features with no associated weight are set to zero. The obtained feature importances from the fitted model are the activities mdt of the regulators in net.

Value

A long format tibble of the enrichment scores for each source across the samples. Resulting tibble contains the following columns:

1. statistic: Indicates which method is associated with which score.

2. source: Source nodes of network.

3. condition: Condition representing each column of mat.

4. score: Regulatory activity (enrichment score).

See Also

Other decoupleR statistics: decouple(), run_aucell(), run_fgsea(), run_gsva(), run_mlm(), run_ora(), run_udt(), run_ulm(), run_viper(), run_wmean(), run_wsum()

Examples

inputs_dir <- system.file("testdata", "inputs", package = "decoupleR")

mat <- readRDS(file.path(inputs_dir, "mat.rds"))
net <- readRDS(file.path(inputs_dir, "net.rds"))

run_mdt(mat, net, minsize=0)

saezlab/decoupleR documentation built on April 12, 2024, 10:41 a.m.