#' download an Rdata object from the recount2 project to be extended to
#' other public RNASeq datasets
#'
#' @param id Id of the study to be downloaded and analysed
#' @return rse_gene An RangedSummarizedExperiment object
load_data <- function(id){
url <- paste0("http://duffel.rail.bio/recount/v2/",id,"/rse_gene.Rdata")
system(paste0("wget ", url))
load("rse_gene.Rdata")
return(rse_gene)
}
#' Get class vector from the rse_gene
#' @param rse_gene an object downloaded from recount
#' @return a character vector of the assigned class
get_class <- function(rse_gene){
class <- vector()
di <- dim(colData(rse_gene))[1]
for (i in 1:di){
class[i] <- as.character(as.data.frame(strsplit(colData(rse_gene)$characteristics[[i]],":"))[2,4])
}
class <- gsub(" ","",class)
keep_class <- which(class %in% c("ColorectalCancer","HealthyControl"))
class2 <- class[keep_class]
return(class2)
}
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