run_viper {decoupleR} | R Documentation |
Calculates regulatory activities using VIPER.
run_viper( mat, network, .source = .data$source, .target = .data$target, .mor = .data$mor, .likelihood = .data$likelihood, verbose = FALSE, minsize = 0, pleiotropy = T, eset.filter = F, ... )
mat |
Matrix to evaluate (e.g. expression matrix).
Target nodes in rows and conditions in columns.
|
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 |
Column with edge likelihood. |
verbose |
Logical, whether progression messages should be printed in the terminal. |
minsize |
Integer indicating the minimum number of targets allowed per regulon. |
pleiotropy |
Logical, whether correction for pleiotropic regulation should be performed. |
eset.filter |
Logical, whether the dataset should be limited only to the genes represented in the interactome . |
... |
Arguments passed on to
|
This function is a wrapper for the method viper::viper()
.
A long format tibble of the enrichment scores for each source across the samples. Resulting tibble contains the following columns:
statistic
: Indicates which method is associated with which score.
source
: Source nodes of network
.
condition
: Condition representing each column of mat
.
score
: Regulatory activity (enrichment score).
Other decoupleR statistics:
decouple()
,
run_aucell()
,
run_fgsea()
,
run_gsva()
,
run_mdt()
,
run_mlm()
,
run_ora()
,
run_udt()
,
run_ulm()
,
run_wmean()
,
run_wsum()
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")) run_viper(mat, network, .source='tf', verbose = FALSE)