getAdjacencyBiogrid {TCGAbiolinks} | R Documentation |
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.
getAdjacencyBiogrid(tmp.biogrid, names.genes = NULL)
tmp.biogrid |
Biogrid table |
names.genes |
List of genes to filter from output. Default: consider all genes |
A matrix with 1 for genes that interacts, 0 for no interaction.
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)