\documentclass[a4paper]{book}
\usepackage[times,hyper]{Rd}
\usepackage{makeidx}
\makeindex{}
\begin{document}
\chapter*{}
\begin{center}
{\textbf{\huge simpIntLists Package}}
\par\bigskip{\large \today}
\end{center}
\Rdcontents{\R{} topics documented:}
\HeaderA{simpIntLists-package}{The package contains BioGRID interactions for various organisms in a simple format}{simpIntLists.Rdash.package}
\aliasA{simpIntLists}{simpIntLists-package}{simpIntLists}
\keyword{package}{simpIntLists-package}
%\VignetteIndexEntry{simpIntLists} 
\begin{Description}\relax
The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, 
mouse, yeast( budding yeast ) and S.pombe (fission yeast) .
Entrez ids, official names and unique ids can be used to find proteins.
\end{Description}
\begin{Details}\relax
\Tabular{ll}{
Package: & simpIntLists\\
Type: & Package\\
Version: & 1.0\\
Date: & 2011-01-18\\
License: & GPL version 2 or newer\\
LazyLoad: & yes\\
}
\end{Details}
\begin{Author}\relax
Kircicegi KORKMAZ, Volkan ATALAY, Rengul CETIN ATALAY
Maintainer: Kircicegi KORKMAZ \textless{}e102771@ceng.metu.edu.tr\textgreater{}
\end{Author}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, 
Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex1>>=
 library(simpIntLists)
 i<-findInteractionList("arabidopsis", "EntrezId")
 i[1:5]
 data(ArabidopsisBioGRIDInteractionUniqueId)
 ArabidopsisBioGRIDInteractionUniqueId[30:32]
@
\end{Examples}

\HeaderA{ArabidopsisBioGRIDInteractionEntrezId}{BioGRID interactions for thale cress (Arabidopsis thaliana), entrez ids are used as identifiers}{ArabidopsisBioGRIDInteractionEntrezId}
\keyword{datasets}{ArabidopsisBioGRIDInteractionEntrezId}
\begin{Description}\relax
This data set contains a list of interactions for  thale cress (Arabidopsis thaliana).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, Entrez ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(ArabidopsisBioGRIDInteractionEntrezId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
List of 2118
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
\$ :List of 2
..\$ name       : int 828230
..\$ interactors: int [1:12] 832208 821860 821860 832208 832208 821860 832208 5888 842783 834532 ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex2>>=
data(ArabidopsisBioGRIDInteractionEntrezId)
ArabidopsisBioGRIDInteractionEntrezId[1:5]
@
\end{Examples}

\HeaderA{ArabidopsisBioGRIDInteractionOfficial}{BioGRID interactions for thale cress (Arabidopsis thaliana), official names are used as identifiers}{ArabidopsisBioGRIDInteractionOfficial}
\keyword{datasets}{ArabidopsisBioGRIDInteractionOfficial}
\begin{Description}\relax
This data set contains a list of interactions for  thale cress (Arabidopsis thaliana).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, official names are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(ArabidopsisBioGRIDInteractionOfficial)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
List of 2109
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
\$ :List of 2
..\$ name       : chr "BRCA2(IV)"
..\$ interactors: chr [1:12] "ATRAD51" "DMC1" "DMC1" "ATRAD51" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex3>>=
data(ArabidopsisBioGRIDInteractionOfficial)
ArabidopsisBioGRIDInteractionOfficial[1:5]
@
\end{Examples}

\HeaderA{ArabidopsisBioGRIDInteractionUniqueId}{BioGRID interactions for thale cress (Arabidopsis thaliana), unique ids are used as identifiers}{ArabidopsisBioGRIDInteractionUniqueId}
\keyword{datasets}{ArabidopsisBioGRIDInteractionUniqueId}
\begin{Description}\relax
This data set contains a list of interactions for  thale cress (Arabidopsis thaliana).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, unique ids (systematic names) are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(ArabidopsisBioGRIDInteractionUniqueId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
List of 2106
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
\$ :List of 2
..\$ name       : chr "At4g00020"
..\$ interactors: chr [1:12] "At5g20850" "At3g22880" "At3g22880" "At5g20850" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex4>>=
data(ArabidopsisBioGRIDInteractionUniqueId)
ArabidopsisBioGRIDInteractionUniqueId[1:5]
@
\end{Examples}

\HeaderA{C.ElegansBioGRIDInteractionEntrezId}{BioGRID interactions for C.elegans (Caenorhabditis elegans), entrez ids are used as identifiers}{C.ElegansBioGRIDInteractionEntrezId}
\keyword{datasets}{C.ElegansBioGRIDInteractionEntrezId}
\begin{Description}\relax
This data set contains a list of interactions for  C.elegans (Caenorhabditis elegans).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, Entrez ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(C.ElegansBioGRIDInteractionEntrezId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
List of 3573
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
\$ :List of 2
..\$ name       : int 177286
..\$ interactors: int [1:4] 179791 178104 180982 178104
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex5>>=
data(C.ElegansBioGRIDInteractionEntrezId)
C.ElegansBioGRIDInteractionEntrezId[1:5]
@
\end{Examples}

\HeaderA{C.ElegansBioGRIDInteractionOfficial}{BioGRID interactions for C.elegans (Caenorhabditis elegans), official names are used as identifiers}{C.ElegansBioGRIDInteractionOfficial}
\keyword{datasets}{C.ElegansBioGRIDInteractionOfficial}
\begin{Description}\relax
This data set contains a list of interactions for  C.elegans (Caenorhabditis elegans).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, official names are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(C.ElegansBioGRIDInteractionOfficial)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
List of 3557
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
\$ :List of 2
..\$ name       : chr "soc-2"
..\$ interactors: chr [1:4] "W07G4.5" "let-60" "bar-1" "let-60"
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex6>>=
data(C.ElegansBioGRIDInteractionOfficial)
C.ElegansBioGRIDInteractionOfficial[1:5]
@
\end{Examples}

\HeaderA{C.ElegansBioGRIDInteractionUniqueId}{BioGRID interactions for C.elegans (Caenorhabditis elegans), unique ids are used as identifiers}{C.ElegansBioGRIDInteractionUniqueId}
\keyword{datasets}{C.ElegansBioGRIDInteractionUniqueId}
\begin{Description}\relax
This data set contains a list of interactions for  C.elegans (Caenorhabditis elegans).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, unique ids(systematic names) are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(C.ElegansBioGRIDInteractionUniqueId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
List of 3571
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
\$ :List of 2
..\$ name       : chr "AC7.2"
..\$ interactors: chr [1:4] "W07G4.5" "ZK792.6" "C54D1.6" "ZK792.6"
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex7>>=
data(C.ElegansBioGRIDInteractionUniqueId)
C.ElegansBioGRIDInteractionUniqueId[1:5]
@
\end{Examples}

\HeaderA{findInteractionList}{Find BioGRID interaction list for a given organism an identifier type}{findInteractionList}
\keyword{file}{findInteractionList}
\begin{Description}\relax
Find BioGRID interaction list for a given organism an identifier type
\end{Description}
\begin{Usage}
\begin{verbatim}
findInteractionList(organism, idType)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{organism}] Organism name. Can be one of 'arabidopsis', 'c.elegans', 'fruitFly', 'human', 'mouse', 'yeast', 's.pombe'. 

\item[\code{idType}] Type of identifier used. Can be one of 'EntrezId', 'Official' and 'UniqueId'
\end{ldescription}
\end{Arguments}
\begin{Value}
List containing the interactions. For each gene/protein, there is an entry in the list with "name" containing name of the gen/protein and "interactors" containing the list of genes/proteins interacting with it.
\end{Value}
\begin{Examples}
<<ex8>>=
 l <- findInteractionList("arabidopsis", "EntrezId")
 l[1:5]
@
\end{Examples}

\HeaderA{FruitFlyBioGRIDInteractionEntrezId}{BioGRID interactions for Fruit fly (Drosophila melanogaster), entrez ids are used as identifiers}{FruitFlyBioGRIDInteractionEntrezId}
\keyword{datasets}{FruitFlyBioGRIDInteractionEntrezId}
\begin{Description}\relax
This data set contains a list of interactions for Fruit fly (Drosophila melanogaster)
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, Entrez ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(FruitFlyBioGRIDInteractionEntrezId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 7578
\$ :List of 2
..\$ name       : int 43383
..\$ interactors: int [1:18] 37006 40877 46391 32132 43584 3355072 39452 40887 40889 47186 ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex9>>=
data(FruitFlyBioGRIDInteractionEntrezId)
FruitFlyBioGRIDInteractionEntrezId[1:5]
@
\end{Examples}

\HeaderA{FruitFlyBioGRIDInteractionOfficial}{BioGRID interactions for Fruit fly (Drosophila melanogaster), official names are used as identifiers}{FruitFlyBioGRIDInteractionOfficial}
\keyword{datasets}{FruitFlyBioGRIDInteractionOfficial}
\begin{Description}\relax
This data set contains a list of interactions for Fruit fly (Drosophila melanogaster)
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, official names are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(FruitFlyBioGRIDInteractionOfficial)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
List of 7577
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
\$ :List of 2
..\$ name       : chr "fkh"
..\$ interactors: chr [1:18] "CG6459" "CG10032" "CG11899" "CkIIbeta" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex10>>=
data(FruitFlyBioGRIDInteractionOfficial)
FruitFlyBioGRIDInteractionOfficial[1:5]
@
\end{Examples}

\HeaderA{FruitFlyBioGRIDInteractionUniqueId}{BioGRID interactions for Fruit fly (Drosophila melanogaster), unique ids (systematic names) are used as identifiers}{FruitFlyBioGRIDInteractionUniqueId}
\keyword{datasets}{FruitFlyBioGRIDInteractionUniqueId}
\begin{Description}\relax
This data set contains a list of interactions for Fruit fly (Drosophila melanogaster)
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, unique ids (systematic names)  are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(FruitFlyBioGRIDInteractionUniqueId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 7563
\$ :List of 2
..\$ name       : chr "Dmel\_CG10002"
..\$ interactors: chr [1:18] "Dmel\_CG6459" "Dmel\_CG10032" "Dmel\_CG11899" "Dmel\_CG15224" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex11>>=
data(FruitFlyBioGRIDInteractionUniqueId)
FruitFlyBioGRIDInteractionUniqueId[1:5]
@
\end{Examples}

\HeaderA{HumanBioGRIDInteractionEntrezId}{BioGRID interactions for human (Homo sapiens), entrez ids are used as identifiers}{HumanBioGRIDInteractionEntrezId}
\keyword{datasets}{HumanBioGRIDInteractionEntrezId}
\begin{Description}\relax
This data set contains a list of interactions for human (Homo sapiens).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, Entrez ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(HumanBioGRIDInteractionEntrezId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 10213
\$ :List of 2
..\$ name       : int 6416
..\$ interactors: int [1:25] 2318 192176 2318 2318 9043 5599 5871 5609 1326 207 ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex12>>=
data(HumanBioGRIDInteractionEntrezId)
HumanBioGRIDInteractionEntrezId[1]
@
\end{Examples}

\HeaderA{HumanBioGRIDInteractionOfficial}{BioGRID interactions for human (Homo sapiens), official names are used as identifiers}{HumanBioGRIDInteractionOfficial}
\keyword{datasets}{HumanBioGRIDInteractionOfficial}
\begin{Description}\relax
This data set contains a list of interactions for human (Homo sapiens).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, official names ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(HumanBioGRIDInteractionOfficial)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 10098
\$ :List of 2
..\$ name       : chr "MAP2K4"
..\$ interactors: chr [1:25] "FLNC" "Flna" "FLNC" "FLNC" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex13>>=
data(HumanBioGRIDInteractionOfficial)
HumanBioGRIDInteractionOfficial[1]
@
\end{Examples}

\HeaderA{HumanBioGRIDInteractionUniqueId}{BioGRID interactions for human (Homo sapiens), unique ids (systematic names) are used as identifiers}{HumanBioGRIDInteractionUniqueId}
\keyword{datasets}{HumanBioGRIDInteractionUniqueId}
\begin{Description}\relax
This data set contains a list of interactions for human (Homo sapiens).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, unique ids (systematic names) are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(HumanBioGRIDInteractionUniqueId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
List of 2785
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
\$ :List of 2
..\$ name       : chr "-"
..\$ interactors: chr "-"
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex14>>=
data(HumanBioGRIDInteractionUniqueId)
HumanBioGRIDInteractionUniqueId[1]
@
\end{Examples}

\HeaderA{MouseBioGRIDInteractionEntrezId}{BioGRID interactions for Mouse (Mus musculus), entrez ids are used as identifiers}{MouseBioGRIDInteractionEntrezId}
\keyword{datasets}{MouseBioGRIDInteractionEntrezId}
\begin{Description}\relax
This data set contains a list of interactions for Mouse (Mus musculus).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, Entrez ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(MouseBioGRIDInteractionEntrezId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 2361
\$ :List of 2
..\$ name       : int 4087
..\$ interactors: int [1:28] 75141 19376 69159 72433 69288 54126 78294 57443 18412 52432 ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex15>>=
data(MouseBioGRIDInteractionEntrezId)
MouseBioGRIDInteractionEntrezId[1:5]
@
\end{Examples}

\HeaderA{MouseBioGRIDInteractionOfficial}{BioGRID interactions for Mouse (Mus musculus), official names ids are used as identifiers}{MouseBioGRIDInteractionOfficial}
\keyword{datasets}{MouseBioGRIDInteractionOfficial}
\begin{Description}\relax
This data set contains a list of interactions for Mouse (Mus musculus).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, official names are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(MouseBioGRIDInteractionOfficial)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 2354
\$ :List of 2
..\$ name       : chr "SMAD2"
..\$ interactors: chr [1:28] "Rasd2" "Rab34" "Rhebl1" "Rab38" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex16>>=
data(MouseBioGRIDInteractionOfficial)
MouseBioGRIDInteractionOfficial[1:5]
@
\end{Examples}

\HeaderA{MouseBioGRIDInteractionUniqueId}{BioGRID interactions for Mouse (Mus musculus), unique ids (systematic names) are used as identifiers}{MouseBioGRIDInteractionUniqueId}
\keyword{datasets}{MouseBioGRIDInteractionUniqueId}
\begin{Description}\relax
This data set contains a list of interactions for Mouse (Mus musculus).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, Entrez ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(MouseBioGRIDInteractionUniqueId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:

List of 648
\$ :List of 2
..\$ name       : chr "-"
..\$ interactors: chr "-"
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex17>>=
data(MouseBioGRIDInteractionUniqueId)
MouseBioGRIDInteractionUniqueId[1:5]
@
\end{Examples}

\HeaderA{S.PombeBioGRIDInteractionEntrezId}{BioGRID interactions for fission yeast (Schizosaccharomyces pombe), entrez ids are used as identifiers}{S.PombeBioGRIDInteractionEntrezId}
\keyword{datasets}{S.PombeBioGRIDInteractionEntrezId}
\begin{Description}\relax
This data set contains a list of interactions for fission yeast (Schizosaccharomyces pombe).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, Entrez ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(S.PombeBioGRIDInteractionEntrezId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 2110
\$ :List of 2
..\$ name       : int 2539495
..\$ interactors: int [1:10] 2541652 2542008 2539252 2541055 2542677 2543539 2541652 2540024 2539649 2542008
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex18>>=
data(S.PombeBioGRIDInteractionEntrezId)
S.PombeBioGRIDInteractionEntrezId[1:5]
@
\end{Examples}

\HeaderA{S.PombeBioGRIDInteractionOfficial}{BioGRID interactions for fission yeast (Schizosaccharomyces pombe), official names are used as identifiers}{S.PombeBioGRIDInteractionOfficial}
\keyword{datasets}{S.PombeBioGRIDInteractionOfficial}
\begin{Description}\relax
This data set contains a list of interactions for fission yeast (Schizosaccharomyces pombe).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, official names are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(S.PombeBioGRIDInteractionOfficial)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 2110
\$ :List of 2
..\$ name       : chr "ptc1"
..\$ interactors: chr [1:10] "sty1" "ptc3" "ptc2" "wis1" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex19>>=
data(S.PombeBioGRIDInteractionOfficial)
S.PombeBioGRIDInteractionOfficial[1:5]
@
\end{Examples}

\HeaderA{S.PombeBioGRIDInteractionUniqueId}{BioGRID interactions for fission yeast (Schizosaccharomyces pombe), unique ids (systematic names) are used as identifiers}{S.PombeBioGRIDInteractionUniqueId}
\keyword{datasets}{S.PombeBioGRIDInteractionUniqueId}
\begin{Description}\relax
This data set contains a list of interactions for fission yeast (Schizosaccharomyces pombe).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, unique ids (systematic names) are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(S.PombeBioGRIDInteractionUniqueId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 2097
\$ :List of 2
..\$ name       : chr "SPCC4F11.02"
..\$ interactors: chr [1:10] "SPAC24B11.06c" "SPAC2G11.07c" "SPCC1223.11" "SPBC409.07c" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex20>>=
data(S.PombeBioGRIDInteractionUniqueId)
S.PombeBioGRIDInteractionUniqueId[1:5]
@
\end{Examples}

\HeaderA{YeastBioGRIDInteractionEntrezId}{BioGRID interactions for budding yeast (Saccharomyces cerevisiae), entrez ids are used as identifiers}{YeastBioGRIDInteractionEntrezId}
\keyword{datasets}{YeastBioGRIDInteractionEntrezId}
\begin{Description}\relax
This data set contains a list of interactions for budding yeast (Saccharomyces cerevisiae).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, Entrez ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(YeastBioGRIDInteractionEntrezId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 6049
\$ :List of 2
..\$ name       : int 850504
..\$ interactors: int [1:887] 852545 853814 856220 853086 850749 853986 856848 851407 856518 854317 ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex21>>=
data(YeastBioGRIDInteractionEntrezId)
YeastBioGRIDInteractionEntrezId[1:5]
@
\end{Examples}

\HeaderA{YeastBioGRIDInteractionOfficial}{BioGRID interactions for budding yeast (Saccharomyces cerevisiae), official names are used as identifiers}{YeastBioGRIDInteractionOfficial}
\keyword{datasets}{YeastBioGRIDInteractionOfficial}
\begin{Description}\relax
This data set contains a list of interactions for budding yeast (Saccharomyces cerevisiae).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, Entrez ids are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(YeastBioGRIDInteractionOfficial)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 6032
\$ :List of 2
..\$ name       : chr "ACT1"
..\$ interactors: chr [1:887] "ALG7" "ASK1" "COG4" "ERG1" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex22>>=
data(YeastBioGRIDInteractionOfficial)
YeastBioGRIDInteractionOfficial[1:5]
@
\end{Examples}

\HeaderA{YeastBioGRIDInteractionUniqueId}{BioGRID interactions for budding yeast (Saccharomyces cerevisiae), unique ids (systematic names) are used as identifiers}{YeastBioGRIDInteractionUniqueId}
\keyword{datasets}{YeastBioGRIDInteractionUniqueId}
\begin{Description}\relax
This data set contains a list of interactions for budding yeast (Saccharomyces cerevisiae).
The interactions are taken from BioGRID version 3.1.72, January 2011 release. 
For gene/protein entries, unique ids (systematic names) are used.
\end{Description}
\begin{Usage}
\begin{verbatim}data(YeastBioGRIDInteractionUniqueId)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is:
A list containing the interactions. For each gene/protein, there is an entry in the list with "name" 
containing name of the gene/protein and "interactors" containing the list of genes/proteins 
interacting with it.
example:
List of 5931
\$ :List of 2
..\$ name       : chr "YFL039C"
..\$ interactors: chr [1:887] "YBR243C" "YKL052C" "YPR105C" "YGR175C" ...
\end{Format}
\begin{Source}\relax
http://thebiogrid.org/download.php
\end{Source}
\begin{References}\relax
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. \emph{Biogrid: A General Repository for Interaction Datasets.} Nucleic Acids Res. Jan1; 34:D535-9
\end{References}
\begin{Examples}
<<ex23>>=
data(YeastBioGRIDInteractionUniqueId)
YeastBioGRIDInteractionUniqueId[1:5]
@
\end{Examples}

\printindex{}
\end{document}
