dot-decoupler_network_format: DecoupleR network format

In saezlab/decoupleR: decoupleR: Ensemble of computational methods to infer biological activities from omics data

DecoupleR network format

Description

A network passed to any run_ method in the package must contain at least two attributes: .source and .target. In addition, the methods must map their corresponding metadata associated with their edges.

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	Deprecated argument. Now it will always be set to 1.

Details

• All the attributes to be mapped are prefixed by .

• The idea of using this type of mapping is to provide flexibility to different types of networks, be they regulatory, metabolic, or of any other type. This way, you should only consider having your network or networks in a long format and these can easily be manipulated by functions within the tidyverse ecosystem.

See Also

Other decoupleR formats: .decoupler_mat_format

saezlab/decoupleR documentation built on April 12, 2024, 10:41 a.m.