getAdjacencyBiogrid {TCGAbiolinks} | R Documentation

## Get a matrix of interactions of genes from biogrid

### Description

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

### 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)

[Package TCGAbiolinks version 2.8.4 Index]