R: Convert a network to run under the method of interest.

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_scira(network, .source, .target, .mor = NULL)

convert_to_pscira(network, .source, .target, .mor = NULL)

convert_to_mean(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)

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

convert_to_ Return same as input.

convert_to_gsva() Return a list of regulons suitable for GSVA::gsva().
convert_to_mean() Return a tibble with four columns: tf, target, mor and likelihood.
convert_to_ora() Return a named list of regulons; tf with associated targets.
convert_to_pscira() Returns a tibble with three columns: tf, target and mor.
convert_to_scira() Returns a tibble with three columns: tf, target and mor.
convert_to_viper() Return a list of regulons suitable for viper::viper()

Examples

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

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

convert_to_(network)
convert_to_gsva(network, tf, target)
convert_to_mean(network, tf, target, mor, likelihood)
convert_to_ora(network, tf, target)
convert_to_pscira(network, tf, target, mor)
convert_to_scira(network, tf, target, mor)
convert_to_viper(network, tf, target, mor, likelihood)