iRefR: iRefIndex Manager
Version 1.13

"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.

Browse man pages Browse package API and functions Browse package files

AuthorAntonio Mora <antoniocmora@gmail.com>, Ian Donaldson <ian.oslo@gmail.com>
Date of publication2013-12-17 19:35:08
MaintainerAntonio Mora <antoniocmora@gmail.com>
LicenseGPL (>= 2)
Version1.13
URL http://irefindex.org/wiki/index.php?title=iRefR
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("iRefR")

Man pages

convert_complexList_to_MITAB: Convert complexList format to MITAB format
convert_edgeList_to_graph: Convert iRefIndex/edgeList table to Graph
convert_edgeList_to_MITAB: Convert edgeList format to MITAB format
convert_graph_to_edgeList: Convert Graph to iRefIndex/edgeList table
convert_MITAB_to_complexList: Convert MITAB format to complexList format
convert_MITAB_to_edgeList: Convert MITAB format to edgeList format
convert_protein_ID: Convert Protein Identifier
create_id_conversion_table: Create a Protein ID Conversion Table
get_irefindex: Get iRefIndex
merge_complexes_lists: Merge tables in complexList Format
select_confidence: Select the subset of iRefIndex corresponding to a set of...
select_database: Select iRefIndex Records belonging to given Primary...
select_interaction_type: Select Binary||Polymer||Complex in iRefIndex
select_protein: Get all iRefIndex records for a given Protein
summary_graph: Get Summary Information for a Graph
summary_protein: Get Summary Information for a given Protein
summary_table: Get Summary Information for a MITAB Table

Functions

convert_MITAB_to_complexList Man page Source code
convert_MITAB_to_edgeList Man page Source code
convert_complexList_to_MITAB Man page Source code
convert_edgeList_to_MITAB Man page Source code
convert_edgeList_to_graph Man page Source code
convert_graph_to_edgeList Man page Source code
convert_protein_ID Man page Source code
create_id_conversion_table Man page Source code
get_irefindex Man page Source code
merge_complexes_lists Man page Source code
select_confidence Man page Source code
select_database Man page Source code
select_interaction_type Man page Source code
select_protein Man page Source code
summary_graph Man page Source code
summary_protein Man page Source code
summary_table Man page Source code

Files

inst
inst/NEWS
inst/doc
inst/doc/iRefR_tutorial.pdf
NAMESPACE
R
R/create_id_conversion_table.R
R/convert_edgeList_to_graph.R
R/merge_complexes_lists.R
R/select_protein.R
R/summary_table.R
R/get_irefindex.R
R/convert_graph_to_edgeList.R
R/convert_edgeList_to_MITAB.R
R/select_database.R
R/summary_graph.R
R/select_confidence.R
R/select_interaction_type.R
R/convert_MITAB_to_complexList.R
R/convert_MITAB_to_edgeList.R
R/convert_complexList_to_MITAB.R
R/convert_protein_ID.R
R/summary_protein.R
MD5
DESCRIPTION
man
man/summary_graph.Rd
man/convert_graph_to_edgeList.Rd
man/select_confidence.Rd
man/convert_MITAB_to_edgeList.Rd
man/summary_table.Rd
man/merge_complexes_lists.Rd
man/summary_protein.Rd
man/convert_edgeList_to_graph.Rd
man/select_protein.Rd
man/select_database.Rd
man/select_interaction_type.Rd
man/convert_edgeList_to_MITAB.Rd
man/create_id_conversion_table.Rd
man/convert_complexList_to_MITAB.Rd
man/get_irefindex.Rd
man/convert_MITAB_to_complexList.Rd
man/convert_protein_ID.Rd
iRefR documentation built on May 19, 2017, 10:34 p.m.