\name{biogridDataDownload}
\alias{biogridDataDownload}
\title{
Download and extract a network interaction matrix from a BioGRID data set 
}
\description{
This function downloads an interaction data set from the BioGRID into
an user-specified folder and extracts an interaction matrix for a given
species. 
}
\usage{
biogridDataDownload(link, species = "Dm", dataDirectory=".", verbose=TRUE)
}
\arguments{
  \item{link}{
the link (url) from where the data should be downloaded (in tab2 format).
If this argument is missing or NULL, the default link (version 3.1.71,
valid on Dec. 5 2010) will be used.
}
  \item{species}{
a single character value specifying the species for which the data should 
be read. The current version supports one of the following species: "Dm" 
("Drosophila_melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus"), 
"Mm" ("Mus_musculus"), "Ce" ("Caenorhabditis_elegans").
}	
  \item{dataDirectory}{
the directory to store downloaded file
}
  \item{verbose}{
a single logical value specifying to display detailed messages (when 
verbose=TRUE) or not (when verbose=FALSE)
}
}
\details{
This function is made to work on the tab2 format from the Biogrid (i.e. 
the first line is a header containing the columns names).
}
\value{
a matrix with one row for each interaction, and three columns: InteractorA, 
InteractorB (both given by their Entrez Identifiers) and InteractionType 
(physical or genetic).
}
\references{
Stark et al. \emph{BioGRID: a general repository for interaction datasets.} 
Nucleic Acids Research 2006 34(Database Issue):D535-D539
}
\author{
Camille Terfve, Xin Wang
}
\seealso{
\code{\link[HTSanalyzeR:networkAnalysis]{networkAnalysis}}, \code{\link[HTSanalyzeR:preprocess]{preprocess}}
}
\examples{
\dontrun{
InteractionsData<-biogridDataDownload(species="Dm", dataDirectory="TestDir", 
verbose=TRUE)
}
}