query_general_value {UCSCXenaShiny}

download data for shiny general analysis

Description

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

## Not run: 
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)

## End(Not run)