getAdjacencyBiogrid: Get a matrix of interactions of genes from biogrid

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Get a matrix of interactions of genes from biogrid

Description

Using biogrid database, it will create a matrix of gene interactions. If columns A and row B has value 1, it means the gene A and gene B interacts.

Usage

getAdjacencyBiogrid(tmp.biogrid, names.genes = NULL)

Arguments

tmp.biogrid	Biogrid table
names.genes	List of genes to filter from output. Default: consider all genes

Value

A matrix with 1 for genes that interacts, 0 for no interaction.

Examples

names.genes.de <- c("PLCB1","MCL1","PRDX4","TTF2","TACC3", "PARP4","LSM1")
tmp.biogrid <- data.frame("Official.Symbol.Interactor.A" = names.genes.de,
                          "Official.Symbol.Interactor.B" = rev(names.genes.de))
net.biogrid.de <- getAdjacencyBiogrid(tmp.biogrid, names.genes.de)
## Not run: 
  file <- paste0("http://thebiogrid.org/downloads/archives/",
                 "Release%20Archive/BIOGRID-3.4.133/BIOGRID-ALL-3.4.133.tab2.zip")
  downloader::download(file,basename(file))
  unzip(basename(file),junkpaths =TRUE)
  tmp.biogrid <- read.csv(gsub("zip","txt",basename(file)),
                          header=TRUE, sep="\t", stringsAsFactors=FALSE)
  names.genes.de <- c("PLCB1","MCL1","PRDX4","TTF2","TACC3", "PARP4","LSM1")
  net.biogrid.de <- getAdjacencyBiogrid(tmp.biogrid, names.genes.de)

## End(Not run)

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.