Nothing
#' @describeIn get_pancan_value Fetch copy number value from CCLE dataset
#' @export
get_ccle_cn_value <- function(identifier) {
host <- "publicHub"
dataset <- "ccle/CCLE_copynumber_byGene_2013-12-03"
res <- check_exist_data(identifier, dataset, host)
if (res$ok) {
data <- res$data
} else {
data <- get_pancan_value(identifier, dataset = dataset, host = host)
save_data(data, identifier, dataset, host)
}
unit <- "log(copy number/2)"
report_dataset_info(dataset)
res <- list(data = data, unit = unit)
res
}
#' @param norm normalization method
#'
#' @describeIn get_pancan_value Fetch gene expression value from CCLE dataset
#' @export
get_ccle_gene_value <- function(identifier, norm = c("rpkm","nc")) {
host <- "publicHub"
if(norm=="rpkm"){
dataset <- "ccle/CCLE_DepMap_18Q2_RNAseq_RPKM_20180502"
} else {
dataset <- "ccle/CCLE_DepMap_18Q2_RNAseq_reads_20180502.log2"
}
res <- check_exist_data(identifier, dataset, host)
if (res$ok) {
expression <- res$data
} else {
expression <- get_pancan_value(identifier, dataset = dataset, host = host)
save_data(expression, identifier, dataset, host)
}
if(norm=="rpkm"){
unit <- "RPKM"
} else {
unit <- "log2(count+1)"
}
report_dataset_info(dataset)
res <- list(expression = expression, unit = unit)
res
}
#' @describeIn get_pancan_value Fetch gene protein expression value from CCLE dataset
#' @export
get_ccle_protein_value <- function(identifier) {
## NOTE: Only ~200 proteins available, so many identifiers will return NAs
host <- "publicHub"
dataset <- "ccle/CCLE_RPPA_20180123"
res <- check_exist_data(identifier, dataset, host)
if (res$ok) {
expression <- res$data
} else {
expression <- get_pancan_value(identifier, dataset = dataset, host = host)
save_data(expression, identifier, dataset, host)
}
unit <- "norm_value"
report_dataset_info(dataset)
res <- list(expression = expression, unit = unit)
res
}
## .p_dataset_field("https://ucscpublic.xenahubs.net", "ccle/CCLE_RPPA_20180123")
## NOTE: this is different from .all_pancan_proteins
.all_ccle_proteins <- c(
"14-3-3_beta", "14-3-3_epsilon_Caution", "14-3-3_zeta", "4E-BP1",
"4E-BP1_pS65", "4E-BP1_pT37_T46", "4E-BP1_pT70", "53BP1", "A-Raf_pS299_Caution",
"ACC1_Caution", "ACC_pS79", "ACVRL1_Caution", "ADAR1", "AMPK_alpha_Caution",
"AMPK_pT172", "AR", "ASNS", "ATM", "Acetyl-a-Tubulin (Lys40)_Caution",
"Akt", "Akt_pS473", "Akt_pT308", "Annexin 1", "Annexin_VII",
"B-Raf_Caution", "B-Raf_pS445", "BRCA2_Caution", "Bad_pS112",
"Bak_Caution", "Bap1 c-4", "Bax", "Bcl-2", "Bcl-xL", "Beclin_Caution",
"Bid_Caution", "Bim(CST2933)", "Bim(EP1036)", "C-Raf(BD610151)_Caution",
"C-Raf(MP05-739)", "C-Raf_pS338", "CD20 _Caution", "CD31", "CD49b",
"CDK1", "Caspase-7_cleavedD198_Caution", "Caspase-8_Caution",
"Caveolin-1", "Chk1_Caution", "Chk1_pS345_Caution", "Chk2", "Chk2_pT68_Caution",
"Claudin-7", "Collagen_VI", "Cyclin_B1", "Cyclin_D1", "Cyclin_E1",
"Cyclin_E2_Caution", "DJ-1", "Di-Ras3_Caution", "Dvl3", "E-Cadherin",
"EGFR", "EGFR_pY1068_Caution", "EGFR_pY1173", "ER-alpha", "ER-alpha_pS118",
"ERCC1_Caution", "ERK2_Caution", "ETS-1", "FASN", "FOXO3a_Caution",
"FOXO3a_pS318_S321_Caution", "FRA1_Caution", "Fibronectin", "FoxM1",
"G6PD", "GAPDH_Caution", "GATA3", "GSK-3-BETA_Caution", "GSK3-alpha-beta",
"GSK3-alpha-beta_pS21_S9", "GSK3_pS9", "Gab2", "HER2", "HER2_pY1248_Caution",
"HER3", "HER3_pY1289_Caution", "HSP70_Caution", "Heregulin",
"IGFBP2", "INPP4B", "IRS1", "JAK2", "JNK2_Caution", "JNK_pT183_Y185",
"Ku80_Caution", "Lck", "MAPK_pT202_Y204", "MDM2_pS166", "MDMX_MDM4(BetIHC-00108)_Caution",
"MEK1", "MEK1_pS217_S221", "MIG-6", "MSH2", "MSH6_Caution", "MYH11",
"Mre11_Caution", "Myosin IIa pS1943", "N-Cadherin", "N-Ras",
"NDRG1_pT346", "NF-kB-p65_pS536_Caution", "NF2_Caution", "Notch1",
"P-Cadherin_Caution", "PAI-1", "PARP_cleaved_Caution", "PCNA_Caution",
"PDCD4_Caution", "PDK1", "PDK1_pS241", "PEA15", "PEA15_pS116",
"PI3K-p110-alpha_Caution", "PI3K-p85", "PKC-alpha", "PKC-alpha_pS657_Caution",
"PKC-delta_pS664", "PKC-pan_BetaII_pS660", "PR", "PRAS40_pT246",
"PRDX1", "PREX1", "PTEN", "Paxillin_Caution", "Porin", "RAD51",
"RBM15", "RSK1-2-3_Caution", "Rab25", "Rad50", "Raptor", "Rb_Caution",
"Rb_pS807_S811", "Rictor_Caution", "Rictor_pT1135", "S6_pS235_S236",
"S6_pS240_S244", "SCD1", "SETD2_Caution", "SF2", "SHP-2_pY542_Caution",
"STAT3_Caution", "STAT3_pY705", "STAT5-alpha", "Shc_pY317", "Smac_Caution",
"Smad1", "Smad3", "Smad4", "Snail_Caution", "Src", "Src_pY416_Caution",
"Src_pY527", "Stathmin", "Syk", "TAZ", "TFRC", "TIGAR", "TSC1_Caution",
"TTF1", "Transglutaminase", "Tuberin", "Tuberin_pT1462", "VAV1_Caution",
"VEGFR2", "VHL_Caution", "XBP1_Caution", "XRCC1_Caution", "YAP_Caution",
"YAP_pS127_Caution", "YB-1", "YB-1_pS102", "alpha-Catenin", "beta Actin_Caution",
"beta-Catenin", "beta-Catenin_pT41_S45", "c-Jun_pS73", "c-Kit",
"c-Met_Caution", "c-Met_pY1235", "c-Myc_Caution", "cIAP_Caution",
"eEF2K", "eEF2_Caution", "eIF4E", "eIF4G_Caution", "mTOR", "mTOR_pS2448_Caution",
"p14 Arf(BetA300-340A)_Caution", "p21", "p27", "p27_pT157_Caution",
"p27_pT198", "p38 alpha MAPK", "p38_MAPK", "p38_pT180_Y182",
"p53_Caution", "p62 Lck ligand_Caution", "p70S6K", "p70S6K_pT389",
"p90RSK_Caution", "p90RSK_pT359_S363_Caution", "p90RSK_pT573_Caution"
)
# NOTE this result is different from get_pancan_mutation_status!
# It is maf like format, needs further processing.
# See ?read.maf to get nonsync mutation
#' @describeIn get_pancan_value Fetch gene mutation info from CCLE dataset
#' @export
get_ccle_mutation_status <- function(identifier) {
if (utils::packageVersion("UCSCXenaTools") < "1.3.2") {
stop("You need to update 'UCSCXenaTools' (>=1.3.2).", call. = FALSE)
}
host <- "https://ucscpublic.xenahubs.net"
dataset <- "ccle/CCLE_DepMap_18Q2_maf_20180502"
report_dataset_info(dataset)
res <- check_exist_data(identifier, dataset, host)
if (res$ok) {
data <- res$data
} else {
query_list <- UCSCXenaTools::fetch_sparse_values(host, dataset, identifier)
data <- as.data.frame(query_list$rows)
data <- dplyr::full_join(
dplyr::tibble(
sampleID = query_list$samples
),
data,
by = "sampleID"
)
save_data(data, identifier, dataset, host)
}
report_dataset_info(dataset)
data
}
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