convert_to_ {decoupleR}R Documentation

Convert a network to run under the method of interest.

Description

Convert a long-format network to the suggested standard for the specified run_{statistic}(). If the default parameters are not modified, then the function sets its own null values for those columns.

Usage

convert_to_(network)

convert_to_aucell(network, .source, .target)

convert_to_ulm(network, .source, .target, .mor = NULL, .likelihood = NULL)

convert_to_mlm(network, .source, .target, .mor = NULL, .likelihood = NULL)

convert_to_wsum(network, .source, .target, .mor = NULL, .likelihood = NULL)

convert_to_wmean(network, .source, .target, .mor = NULL, .likelihood = NULL)

convert_to_viper(network, .source, .target, .mor = NULL, .likelihood = NULL)

convert_to_gsva(network, .source, .target)

convert_to_ora(network, .source, .target)

convert_to_fgsea(network, .source, .target)

Arguments

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.

Value

See Also

convert_f_defaults()

Examples

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

network <- readRDS(file.path(inputs_dir, "input-dorothea_genesets.rds"))

convert_to_(network)
convert_to_aucell(network, tf, target)
convert_to_gsva(network, tf, target)
convert_to_wmean(network, tf, target, mor, likelihood)
convert_to_ora(network, tf, target)
convert_to_wsum(network, tf, target, mor)
convert_to_ulm(network, tf, target, mor)
convert_to_mlm(network, tf, target, mor)
convert_to_viper(network, tf, target, mor, likelihood)

[Package decoupleR version 2.0.0 Index]