R/get_pcawg_value.R

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

# PCAWG -------------------------------------------------------------------

# Not all gene data available
# query_pancan_value("KRAS", database = "pcawg")
# query_pancan_value("hsa-let-7c-3p", database = "pcawg", data_type = "miRNA")
# query_pancan_value("hsa-let-7c-3p", database = "pcawg", data_type = "miRNA", norm_method = "UQ")
# query_pancan_value("ENSG00000000419", database = "pcawg", data_type = "fusion") # gene symbol also work
# query_pancan_value("tCa_MutLoad_MinEstimate", database = "pcawg", data_type = "APOBEC")
# query_pancan_value("prmtr.10000", database = "pcawg", data_type = "promoter")
# query_pancan_value("X:99891803:TSPAN6", database = "pcawg", data_type = "promoter")

#' @describeIn get_pancan_value Fetch specimen-level gene expression value from PCAWG cohort
#' @export
get_pcawg_gene_value <- function(identifier) {
  host <- "pcawgHub"
  dataset <- "tophat_star_fpkm_uq.v2_aliquot_gl.sp.log"

  expression <- get_data(dataset, identifier, host)
  unit <- "log2(fpkm-uq+0.001)"
  report_dataset_info(dataset)
  res <- list(data = expression, unit = unit)
  res
}

#' @describeIn get_pancan_value Fetch specimen-level gene fusion value from PCAWG cohort
#' @export
get_pcawg_fusion_value <- function(identifier) {
  host <- "pcawgHub"
  dataset <- "pcawg3_fusions_PKU_EBI.gene_centric.sp.xena"

  expression <- get_data(dataset, identifier, host)
  unit <- "binary fusion call, 1 fusion, 0 otherwise"
  report_dataset_info(dataset)
  res <- list(data = expression, unit = unit)
  res
}

#' @describeIn get_pancan_value Fetch specimen-level gene promoter activity value from PCAWG cohort
#' @export
get_pcawg_promoter_value <- function(identifier, type = c("raw", "relative", "outlier")) {
  # promoter identifier prmtr.10000 or symbol are supported
  # but the latter seems meaningless
  host <- "pcawgHub"
  type <- match.arg(type)

  if (type == "raw") {
    dataset <- "rawPromoterActivity.sp"
    unit <- "raw promoter activity"
  } else if (type == "relative") {
    dataset <- "relativePromoterActivity.sp"
    unit <- "portion of transcription activity of the gene driven by the promoter"
  } else {
    dataset <- "promoterCentricTable_0.2_1.0.sp"
    unit <- "-1 (low expression), 0 (normal), 1 (high expression)"
  }

  if (!startsWith(identifier, "prmtr")) {
    # Try parsing from location:symbol map
    map <- load_data("pcawg_promoter_id")
    id_map <- map[names(map) == identifier]
    if (length(id_map) > 1) {
      # query_pancan_value("19:12203078:ZNF788", database = "pcawg", data_type = "promoter")
      # 存在极少数有多 id 情况，直接求和
      expression <- purrr::reduce(
        purrr::map(
          as.character(id_map),
          ~ get_data(dataset, ., host)
        ), `+`
      )
    } else {
      expression <- get_data(dataset, as.character(id_map), host)
    }
  } else {
    expression <- get_data(dataset, identifier, host)
  }


  report_dataset_info(dataset)
  res <- list(data = expression, unit = unit)
  res
}

#' @param norm_method the normalization method.
#' @describeIn get_pancan_value Fetch specimen-level miRNA value from PCAWG cohort
#' @export
get_pcawg_miRNA_value <- function(identifier, norm_method = c("TMM", "UQ")) {
  host <- "pcawgHub"
  norm_method <- match.arg(norm_method)

  if (norm_method == "TMM") {
    dataset <- "x3t2m1.mature.TMM.mirna.matrix.log"
    unit <- "log2(cpm-TMM+0.1)"
  } else {
    dataset <- "x3t2m1.mature.UQ.mirna.matrix.log"
    unit <- "log2(cpm-uq+0.1)"
  }

  expression <- get_data(dataset, identifier, host)
  report_dataset_info(dataset)
  res <- list(data = expression, unit = unit)
  res
}


#' @describeIn get_pancan_value Fetch specimen-level gene fusion value from PCAWG cohort
#' @export
get_pcawg_APOBEC_mutagenesis_value <- function(identifier = c(
                                                 "tCa_MutLoad_MinEstimate", "APOBECtCa_enrich",
                                                 "A3A_or_A3B", "APOBEC_tCa_enrich_quartile", "APOBECrtCa_enrich",
                                                 "APOBECytCa_enrich", "APOBECytCa_enrich-APOBECrtCa_enrich",
                                                 "BH_Fisher_p-value_tCa", "ntca+tgan", "rtCa_to_G+rtCa_to_T",
                                                 "rtca+tgay", "tCa_to_G+tCa_to_T",
                                                 "ytCa_rtCa_BH_Fisher_p-value", "ytCa_rtCa_Fisher_p-value", "ytCa_to_G+ytCa_to_T",
                                                 "ytca+tgar"
                                               )) {
  identifier <- match.arg(identifier)
  host <- "pcawgHub"
  dataset <- "MAF_Aug31_2016_sorted_A3A_A3B_comparePlus.sp"

  expression <- get_data(dataset, identifier, host)
  unit <- ""
  report_dataset_info(dataset)
  res <- list(data = expression, unit = unit)
  res
}

## 突变数据直接用表格展示??