Skip to main content

Table 1 Functions in the iRefR package.

From: iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database

name

description

get_irefindex

Retrieve an iRefIndex data set by taxon identifier or release number as a data frame in MITAB format.

*create_id_conversion_table

Use an iRefIndex data set to generate a lookup table that can be used by convert_protein_ID.

*convert_protein_ID

Convert protein identifiers from one of the following formats: iROG ID, icROG ID, gene ID, RefSeq, PDB and UniProt, to any other protein identifier type in the list.

select_interaction_type

Select a subset of MITAB belonging to a certain interaction type (binary, polymer, complex).

select_database

Select (or exclude) a subset of MITAB belonging to one or a group of primary interaction databases.

select_protein

Select a subset of MITAB for a given protein identifier.

select_confidence

Select a subset of MITAB given a confidence or bibliometric score type and value (or value range).

convert_MITAB_to_edgeList

Convert MITAB data set to edgeList format. Can specify complex representation, directionality, node id type (iROG or icROG) and edge-weight.

convert_edgeList_to_MITAB

Retrieves subset of a MITAB data set matching an edgeList. User should specify node identifier type (iROG or icROG) used in edge list. Can specify interaction type to retrieve (binary, complex, polymer).

convert_MITAB_to_complexList

Convert MITAB data set to complexList format. Can specify node id type (iROG or icROG). Can specify if and how potential spoke-represented complexes should be included.

convert_complexList_to_MITAB

Retrieves subset of a MITAB data set matching a complexList. User should specify node identifier type (iROG or icROG) used in complex. Can specify whether potential spoke represented complex lines should be returned.

*merge_complexes_lists

Merge complexLists and remove duplicate complexes.

convert_edgeList_to_graph

Convert an edgeList table to a Graph object. Can specify if edges have directionality and graph package (graph/igraph) that will use the Graph object.

convert_graph_to_edgeList

Convert a Graph to an edgeList table.

summary_protein

Get Summary Information for a given Protein.

summary_table

Get Summary Information for a MITAB Table.

summary_graph

Get Summary Information for a Graph.

  1. *Not shown in Figure 1. All other functions and their relation to input and output data types are shown in Figure 1.