.fit_preprocessing {decoupleR}R Documentation

Pre-processing for methods that fit networks.

Description

Usage

.fit_preprocessing(network, mat, center, na.rm, sparse)

Arguments

network

Tibble or dataframe with edges and it's associated metadata.

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.

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()?

sparse

Deprecated parameter.

Value

A named list of matrices to evaluate in methods that fit models, like .mlm_analysis().

Examples

inputs_dir <- system.file("testdata", "inputs", package = "decoupleR")
mat <- readRDS(file.path(inputs_dir, "input-expr_matrix.rds"))
network <- readRDS(file.path(inputs_dir, "input-dorothea_genesets.rds"))
network <- rename_net(network, tf, target, mor, likelihood)
.fit_preprocessing(network, mat, center = FALSE, na.rm = FALSE, sparse = FALSE)

[Package decoupleR version 2.0.1 Index]