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) {
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)
}