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iRefR (version 1.13)

iRefIndex Manager

Description

"iRefR" allows the user to load any version of the consolidated protein interaction database "iRefIndex" and perform tasks such as: selecting databases, pmids, experimental methods, searching for specific proteins, separate binary interactions from complexes and polymers, generate complexes according to an algorithm that looks after possible binary-represented complexes, make general database statistics and create network graphs, among others.

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Version

Install

install.packages('iRefR')

Monthly Downloads

21

Version

1.13

License

GPL (>= 2)

Maintainer

Antonio Mora

Last Published

December 17th, 2013

Functions in iRefR (1.13)

convert_edgeList_to_MITAB

Convert edgeList format to MITAB format
select_confidence

Select the subset of iRefIndex corresponding to a set of confidence scores
select_protein

Get all iRefIndex records for a given Protein
summary_protein

Get Summary Information for a given Protein
summary_graph

Get Summary Information for a Graph
convert_protein_ID

Convert Protein Identifier
create_id_conversion_table

Create a Protein ID Conversion Table
select_interaction_type

Select Binary||Polymer||Complex in iRefIndex
convert_edgeList_to_graph

Convert iRefIndex/edgeList table to Graph
merge_complexes_lists

Merge tables in complexList Format
select_database

Select iRefIndex Records belonging to given Primary Interaction Databases
convert_MITAB_to_complexList

Convert MITAB format to complexList format
convert_graph_to_edgeList

Convert Graph to iRefIndex/edgeList table
get_irefindex

Get iRefIndex
summary_table

Get Summary Information for a MITAB Table
convert_complexList_to_MITAB

Convert complexList format to MITAB format
convert_MITAB_to_edgeList

Convert MITAB format to edgeList format