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

Description Usage Arguments Value Examples

View source: R/query_value.R

Description

Query Single Identifier or Signature Value from Pan-cancer Database

Usage

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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

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## 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 Nov. 29, 2021, 9:06 a.m.