R/simplifyGOReqData.R

In JoWatson2011/R4JW: What the Package Does (One Line, Title Case)

#' Gather data required for simplify() function, to reduce
#' semantically similar GO terms
#'
#' @return List of dataframes
#' @importFrom org.Hs.eg.db org.Hs.eg.db org.Hs.egGO2EG
#' @importFrom GO.db GO.db GOBPCHILDREN
#' @importFrom GOSemSim godata
#' @importFrom AnnotationDbi select keys
#' @importFrom utils stack unstack
#' @importFrom rlang .data
#' @export
#'
#' @examples simplifyGOReqData()
simplifyGOReqData <- function(){

  if(length(grep("simplifyGOreqdata.rds", list.files("data/"))) < 1) {

    gene2GOi<- AnnotationDbi::select(org.Hs.eg.db,
                                     keys(org.Hs.egGO2EG),
                                     c("ENTREZID", "SYMBOL"),  "GOALL") %>%
      filter(.data$ONTOLOGYALL == "BP")
    gene2GO <- unstack(gene2GOi[,c(1,5)])

    GOterms <- AnnotationDbi::select(GO.db,
                                     keys=gene2GOi$GOALL,
                                     columns=c("TERM"),
                                     keytype = "GOID")

    GO2Gene<-unstack(stack(gene2GO)[2:1])

    freq <- sapply(GO2Gene,length)
    freqCutOff <- length(gene2GO)*0.05
    highFreqTerms <- names(freq[freq>freqCutOff])

    semData <- godata("org.Hs.eg.db","SYMBOL","BP")

    childTerms <- as.list(GOBPCHILDREN)

    saveRDS(list(gene2GO = gene2GO,
                 GOterms=GOterms,
                 GO2Gene=GO2Gene,
                 highFreqTerms=highFreqTerms,
                 semData = semData,
                 childTerms=childTerms),
            "data/simplifyGOreqdata.rds")

    return(list(gene2GO = gene2GO,
                GOterms=GOterms,
                GO2Gene=GO2Gene,
                highFreqTerms=highFreqTerms,
                semData = semData,
                childTerms=childTerms))

  }else{
    return(readRDS("data/simplifyGOreqdata.rds"))
  }
}