Nothing
# 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 = "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 the normalization method.
#' @describeIn get_pancan_value Fetch specimen-level miRNA value from PCAWG cohort
#' @export
get_pcawg_miRNA_value <- function(identifier, norm = c("TMM", "UQ")) {
host <- "pcawgHub"
norm <- match.arg(norm)
if (norm == "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??
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