make_connection {DrDimont}

Specify connection between two individual layers

Description

Helper function to transform input data to the required pipeline input format. This helper function creates a list that specifies the connection between two layers. The connection can be based on IDs present in the identifiers of both layer or an interaction table containing a mapping of the connections and edge weights. Additionally, the supplied input is checked. Allows easy conversion of raw data into the structure accepted by run_pipeline.

__IMPORTANT:__ If a connection is established based on id this ID has to be present in the identifiers of both layers, they have to be named identically and the IDs have to be formatted identically as these are matched by an inner join operation (refer to make_layer).

Usage

make_connection(from, to, connect_on, weight = 1, group = "both")

Arguments

from

[string] Name of the layer from which the connection should be established

to

[string] Name of the layer to which the connection should be established

connect_on

[string|table] Specifies how the two layers should be connected. This can be based on a mutual ID or a table specifying interactions. Mutual ID: Character string specifying the name of an identifier that is present in both layers (e.g., 'NCBI ID' to connect proteins and mRNA). Interaction table: A table mapping two identifiers of two layers. The columns have exactly the same names as the identifiers of the layers. The table has to contain an additional column specifying the weight between two components/nodes (see 'weight' argument)

weight

[int|string] Specifies the edge weight between the layers. This can be supplied as a number applied to every connection or a column name of the interaction table. Fixed weight: A umber specifying the weight of every connection between the layers. Based on interaction table: Character string specifying the name of a column in the table passed as the 'by' parameter which is used as edge weight. (default: 1)

group

["A"|"B"|"both"] Group for which to apply the connection. One of 'both', 'A' or 'B'. (default: "both")

Value

A named list (i.e., an inter-layer connection), that can be supplied to run_pipeline.

Examples

data(metabolite_protein_interactions)

example_inter_layer_connections = list(make_connection(from='mrna', to='protein',
                                           connect_on='gene_name', weight=1),
                                       make_connection(from='protein', to='phosphosite',
                                           connect_on='gene_name', weight=1),
                                       make_connection(from='protein', to='metabolite',
                                           connect_on=metabolite_protein_interactions,
                                           weight='combined_score'))