.fit_preprocessing {decoupleR} | R Documentation |
If center
is true, then the expression values are centered by the
mean of expression across the samples.
.fit_preprocessing(network, mat, center, na.rm, sparse)
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.
|
center |
Logical value indicating if |
na.rm |
Should missing values (including NaN) be omitted from the
calculations of |
sparse |
Deprecated parameter. |
A named list of matrices to evaluate in methods that fit models, like
.mlm_analysis()
.
mat: Features as rows and samples as columns.
mor_mat: Features as rows and columns as source.
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)