R/annotate_fusion_calls.R

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

#' Function to annotate fusion calls

#' @param standardFusioncalls A dataframe from star fusion or arriba standardized to run through the filtering steps
#' @param geneListReferenceDataTab A dataframe with column 1 as GeneName 2 source file 3 type; collapse to summarize type
#' @param fusionReferenceDataTab A dataframe with column 1 as FusionName 2 source file 3 type; collapse to summarize type
#' @param checkReciprocal Logical value to check if fusion also has reciprocal fusion in Sample, default to TRUE
#'
#' @export
#'
#' @return Standardized fusion calls annotated with gene list and fusion list provided in reference folder. If checkReciprocal ==TRUE reciprocal status of fusion is also provided .
#'
#' @examples
#' # standardize
#' fusionfileArriba <- read_arriba_calls(
#'   system.file("extdata", "arriba_example.tsv", package = "annoFuseData")
#' )
#' fusionfileStarFusion <- read_starfusion_calls(
#'   system.file("extdata", "starfusion_example.tsv", package = "annoFuseData")
#' )
#' formattedArriba <- fusion_standardization(fusionfileArriba,
#'   caller = "ARRIBA",
#'   tumorID = "tumorID"
#' )
#' formattedStarFusion <- fusion_standardization(fusionfileStarFusion,
#'   caller = "STARFUSION",
#'   tumorID = "tumorID"
#' )
#' # merge standardized fusion calls
#' standardFusioncalls <- as.data.frame(rbind(formattedStarFusion, formattedArriba))
#' fusionQCFiltered <- fusion_filtering_QC(
#'   standardFusioncalls = standardFusioncalls,
#'   readingFrameFilter = "in-frame|frameshift|other",
#'   artifactFilter = "GTEx_Recurrent|DGD_PARALOGS|Normal|BodyMap|ConjoinG",
#'   junctionReadCountFilter = 1,
#'   spanningFragCountFilter = 10,
#'   readthroughFilter = TRUE
#' )
#' # annotated from gene and fusion refrence list
#' # read in gene and fusion reference tab
#' geneListReferenceDataTab <- read.delim(
#'   system.file("extdata", "genelistreference.txt", package = "annoFuseData"),
#'   stringsAsFactors = FALSE
#' )
#' # column 1 as FusionName 2 source file 3 type; collapse to summarize type
#' fusionReferenceDataTab <- read.delim(
#'   system.file("extdata", "fusionreference.txt", package = "annoFuseData"),
#'   stringsAsFactors = FALSE
#' )
#'
#' filteredFusionAnnotated <- annotate_fusion_calls(
#'   standardFusioncalls = fusionQCFiltered,
#'   geneListReferenceDataTab = geneListReferenceDataTab,
#'   fusionReferenceDataTab = fusionReferenceDataTab,
#'   checkReciprocal = TRUE
#' )
annotate_fusion_calls <- function(standardFusioncalls,
                                  geneListReferenceDataTab,
                                  fusionReferenceDataTab,
                                  checkReciprocal = TRUE) {
  standardFusioncalls <- .check_annoFuse_calls(standardFusioncalls)

  stopifnot(is(geneListReferenceDataTab, "data.frame"))
  stopifnot(is(fusionReferenceDataTab, "data.frame"))
  stopifnot(is.logical(checkReciprocal))

  if (checkReciprocal & nrow(standardFusioncalls) > 0) {
    # check for fusions have reciprocal fusions in the same Sample
    # works only for GeneY -- GeneX ; GeneX -- GeneY matches
    recirpocal_fusion <- function(FusionName, Sample, standardFusioncalls) {
      Gene1A <- strsplit(FusionName, "--")[[1]][1]
      Gene1B <- strsplit(FusionName, "--")[[1]][2]
      reciprocal <- paste0(Gene1B, "--", Gene1A)
      check <- any(standardFusioncalls$FusionName[standardFusioncalls$Sample == Sample] == reciprocal)
      df <- data.frame("FusionName" = FusionName, "Sample" = Sample, "reciprocal_exists" = check)
    }

    # run reciprocal_fusion function to get status of fusion if reciprocal
    is_reciprocal <- apply(standardFusioncalls, 1, function(x) recirpocal_fusion(x["FusionName"], x["Sample"], standardFusioncalls))

    # convert list to dataframe
    is_reciprocal <- data.frame(Reduce(rbind, is_reciprocal))

    # merge to standardized fusion calls
    standardFusioncalls <- standardFusioncalls %>%
      dplyr::left_join(is_reciprocal, by = c("Sample", "FusionName"))
  } else if (checkReciprocal & nrow(standardFusioncalls) == 0) {
    standardFusioncalls$reciprocal_exists <- logical()
  }

  geneListReferenceDataTab <- geneListReferenceDataTab %>% dplyr::select(-file)
  fusionReferenceDataTab <- fusionReferenceDataTab %>% dplyr::select(-file)
  annotated_filtered_fusions <- standardFusioncalls %>%
    # annotate Gene1A
    dplyr::left_join(geneListReferenceDataTab, by = c("Gene1A" = "Gene_Symbol")) %>%
    dplyr::rename(Gene1A_anno = .data$type) %>%
    # annotate Gene1B
    dplyr::left_join(geneListReferenceDataTab, by = c("Gene1B" = "Gene_Symbol")) %>%
    dplyr::rename(Gene1B_anno = .data$type) %>%
    # annotate Gene2A
    dplyr::left_join(geneListReferenceDataTab, by = c("Gene2A" = "Gene_Symbol")) %>%
    dplyr::rename(Gene2A_anno = .data$type) %>%
    # annotate Gene2B
    dplyr::left_join(geneListReferenceDataTab, by = c("Gene2B" = "Gene_Symbol")) %>%
    dplyr::rename(Gene2B_anno = .data$type) %>%
    # annotate FusionName
    dplyr::left_join(fusionReferenceDataTab, by = c("FusionName" = "FusionName")) %>%
    dplyr::rename(Fusion_anno = .data$type) %>%
    as.data.frame()
  annotated_filtered_fusions <- unique(annotated_filtered_fusions)

  return(annotated_filtered_fusions)
}