query_pancan_value: Query Single Identifier or Signature Value from Pan-cancer...

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

Query Single Identifier or Signature Value from Pan-cancer Database

Description

Query Single Identifier or Signature Value from Pan-cancer Database

Usage

query_pancan_value(
  molecule,
  data_type = c("mRNA", "transcript", "protein", "mutation", "cnv", "cnv_gistic2",
    "methylation", "miRNA", "fusion", "promoter", "APOBEC"),
  database = c("toil", "ccle", "pcawg"),
  reset_id = NULL,
  ...
)

Arguments

molecule	a molecular identifier (e.g., "TP53") or a formula specifying genomic signature ("TP53 + 2 * KRAS - 1.3 * PTEN").
data_type	data type. Can be one of "mRNA", "transcript", "protein", "mutation", "cnv" (-2, -1, 0, 1, 2), "cnv_gistic2", "methylation", "miRNA".
database	database, either 'toil' for TCGA TARGET GTEx, or 'ccle' for CCLE.
reset_id	if not NULL, set the specified variable at parent frame to "Signature".
...	other extra parameters passing to the underlying functions.

Value

a list.

Examples

## Not run: 
query_pancan_value("KRAS")
query_pancan_value("KRAS", database = "ccle")
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_method = "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"
)

## End(Not run)

UCSCXenaShiny documentation built on March 7, 2023, 7 p.m.