Download data for shiny general analysis

Usage

query_general_value(
  L1,
  L2,
  L3,
  database = c("toil", "pcawg", "ccle"),
  tpc_value_nonomics = NULL,
  opt_pancan = NULL,
  custom_metadata = NULL
)

Arguments

L1: level 1 main datatype
L2: level 2 sub datatype
L3: level 3 identifier
database: one of c("toil","pcawg","ccle")
tpc_value_nonomics: non-omics matrix data of one database
opt_pancan: molecular datasets parameters
custom_metadata: user customized metadata

Examples

if (FALSE) { # \dontrun{
general_value_id <- UCSCXenaShiny:::query_general_id()
tcga_value_option <- general_value_id[["value"]][[1]]
tcga_index_value <- tcga_value_option[["Tumor index"]]
tcga_immune_value <- tcga_value_option[["Immune Infiltration"]]
tcga_pathway_value <- tcga_value_option[["Pathway activity"]]
tcga_phenotype_value <- tcga_value_option[["Phenotype data"]]

clinical_phe = tcga_phenotype_value[["Clinical Phenotype"]]
x_data = UCSCXenaShiny:::query_general_value(
           "Molecular profile", "mRNA Expression", "TP53", "toil",
           tcga_index_value, tcga_immune_value, tcga_pathway_value,
           clinical_phe)

y_data = UCSCXenaShiny:::query_general_value(
           "Immune Infiltration", "CIBERSORT", "Monocyte", "toil",
           tcga_index_value, tcga_immune_value, tcga_pathway_value,
           clinical_phe)
} # }