R/ont_fun_search.R

In csetraynor/iclust2prog: Prognostic modeling of IntClust-2 (iclust2prog)

#' Examine Ontology
#'
#' Check list of Ontology to find genes relevant assessed by cancer biology.
#' @param
#' hallmark_list: list of hallmarks from ontology database \cr
#' predictor: feature list \cr
#' coeff : TRUE return hazard coefficient
#'
#' @return predicted linear predictor for each individual in the test set
#' @export
#' @importFrom magrittr %>%
#' @importFrom rlang !!

ontology_search <- function(ont, gene_list, coeff = FALSE, coef = median_coeff, name = "hazard ratio"){

  ont <- tolower(ont)
  ont <- qusage::read.gmt(  paste0("docs/Gene sets/", ont, ".all.v6.1.entrez.gmt"))

  coef <- dplyr::enquo(coef)

  p <- gene_list$Entrez_Gene_Id
  hall <- lapply(ont, function(x){
    sapply(p, function(p)
      ifelse(p %in% x, p, NA)
    )
  }
  )
  hall <- lapply(hall, function(x)  x[!is.na(x)])
  hall <- hall[sapply(hall, length)>0]

  if(coeff){
    hall <- lapply(hall, function(h){
      sapply(h, function(i){
        predictor %>% filter(!!Predictor == i) %>% dplyr::select(!!coef)
      })
    })
    hall <- lapply(hall, function(h){
      data.frame( features =  gsub("\\..*","",names(h) ),
                  coef = unlist(h), row.names = NULL)
    })
  }else{
    hall <- lapply(hall, function(h) unname(h))
  }
  return(hall)
}