Reciprocal best hit graph

This class can be used to generate reciprocal best hit graphs between gene modules from different origins.

Usage

RbhGraph(
  module_results,
  rbh_type = c("cor", "set"),
  dataset_col = NULL,
  module_col = NULL,
  value_col = NULL
)

Arguments

module_results

data.table or list. If data.table (you set the class to "set", i.e., set similarities will be used) it cointains all of the gene modules for which you wish to generate the RBH graph and you need to have the three column names. If list (you set the class to `"cor"“, i.e., correlations between for example gene loadings will be used), the list contains all of the matrices (must have col and row names).

rbh_type

String. One of c("cor", "set").

dataset_col

The column (name) which indicates from which data set/ method the gene module was derived. Only needed if you want to use set similarities.

module_col

The column (name) which stores the names of the modules. Only needed if you want to use set similarities.

value_col

The column (name) which stores the genes that are part of the modules. Only needed if you want to use set similarities.

Value

Returns the RbhGraph class for further operations.

Properties

module_data

Nested list of the modules generated by different methods.

rbh_graph

igraph. The reciprocal best hit graph.

rbh_edge_df

data.table. Contains the RBH graph data as an edge df.

params

A (nested) list that will store all the parameters of the applied function.

final_results

data.table. Contains final results.