--- a +++ b/R/PPI.R @@ -0,0 +1,23 @@ +#' @title Defining protein-protein interactions (PPI) over a list of genes, +#' @description This function uses STRING-api. The outcome of STRING analysis +#' will be stored in comma-separated values files. +#' @export +#' @param data A gene list. +#' @param FileName A string vector showing the name to be used to save the +#' resulted table. If null, no file will be exported +#' @param species The taxonomy name/id. Default is "9606" for Homo sapiens. +#' @importFrom httr content +#' @importFrom utils read.table write.table +#' @return Either CSV files stored in the user's file system and its +#' corresponding `data.frame` object in R or and R object containing that +#' information. +PPI <- function(data, FileName = NULL, species = "9606") { + repos <- retrieveURL(data, species, "tsv") + # Process API request content + repo_content <- content(repos) + results <- data.frame(repo_content[, , 1]) + if (!is.null(FileName)) { + write.csv(results, file = paste0("PPI-", FileName, ".csv")) + } + return(results) +}