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. |