R/groupcount_fusion_calls.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 group column name in input standard fusion calls that should be used to identify subset the sample belongs to in the cohort
#' @param numGroup Least number of groups that have the fusion to categories as false call in cohort
#'
#' @export
#'
#' @return Fusions found in more than n groups in cohort
#'
#' @examples
#' out_annofuse <- system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
#' sfc <- read.delim(out_annofuse)
#' sfc_groupcount <- groupcount_fusion_calls(sfc, group = "Sample", 1)
groupcount_fusion_calls <- function(standardFusioncalls,
                                    group,
                                    numGroup) {
  standardFusioncalls <- .check_annoFuse_calls(standardFusioncalls)
  stopifnot(group %in% colnames(standardFusioncalls))
  stopifnot(is.numeric(numGroup))

  # remove fusions that are in > numGroup
  group.count <- standardFusioncalls %>%
    dplyr::select(.data$FusionName, !!as.name(group)) %>%
    unique() %>%
    group_by(.data$FusionName) %>%
    dplyr::mutate(group.ct = n(), Groups = toString(!!(as.name(group)))) %>%
    dplyr::select(-group) %>%
    unique() %>%
    dplyr::filter(.data$group.ct > numGroup)

  return(group.count)
}