R/called_by_n_callers.R

In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

#' Function to identify fusions called by at least n callers
#'
#' @param standardFusioncalls A dataframe from star fusion or arriba standardized
#' to run through the filtering steps
#' @param numCaller Least number of callers that have the fusion
#'
#' @export
#'
#' @return Fusions called by n callers
#'
#' @examples
#' out_annofuse <- system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
#' sfc <- read.delim(out_annofuse)
#' sfc_called <- called_by_n_callers(sfc, numCaller = 2)
called_by_n_callers <- function(standardFusioncalls,
                                numCaller) {
  standardFusioncalls <- .check_annoFuse_calls(standardFusioncalls)
  stopifnot(is.numeric(numCaller))

  # aggregate caller per Sample,FusionName and Fusion_Type
  fusion_caller.summary <- standardFusioncalls %>%
    dplyr::select(.data$Sample, .data$FusionName, .data$Caller, .data$Fusion_Type) %>%
    group_by(.data$FusionName, .data$Sample, .data$Fusion_Type) %>%
    unique() %>%
    dplyr::mutate(CalledBy = toString(.data$Caller), caller_count = n())

  # Called by at least n callers
  fusion_calls.summary <- fusion_caller.summary %>%
    dplyr::filter(.data$caller_count >= numCaller) %>%
    unique() %>%
    mutate(note = paste0("Called by ", numCaller, " callers")) %>%
    as.data.frame()

  return(fusion_calls.summary)
}