run_mlm: Multivariate Linear Model (MLM)

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

Multivariate Linear Model (MLM)

Description

Calculates regulatory activities using MLM.

Usage

run_mlm(
  mat,
  network,
  .source = source,
  .target = target,
  .mor = mor,
  .likelihood = likelihood,
  sparse = FALSE,
  center = FALSE,
  na.rm = FALSE,
  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()?
minsize	Integer indicating the minimum number of targets per source.

Details

MLM fits a multivariate linear model 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 t-values from the fitted model are the activities (mlm) 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_mdt(), 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_mlm(mat, net, minsize=0)

saezlab/decoupleR documentation built on Oct. 21, 2024, 8:47 a.m.