biogridDataDownload: Download and extract a network interaction matrix from a...

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

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

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 3.1.89, valid on Jun. 11 2012) will be used.
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").
dataDirectory	the directory to store downloaded file
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).

Author(s)

Camille Terfve, Xin Wang

References

Stark et al. BioGRID: a general repository for interaction datasets. Nucleic Acids Research 2006 34(Database Issue):D535-D539

See Also

networkAnalysis, preprocess

Examples

## Not run: 
InteractionsData<-biogridDataDownload(species="Dm", dataDirectory="TestDir", 
verbose=TRUE)

## End(Not run)

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.