Query Single Identifier or Signature Value from Pan-cancer Database

Query Single Identifier or Signature Value from Pan-cancer Database

Usage

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

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", "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".

opt_pancan

other extra parameters passing to the underlying functions.

Value

a list.

Details

query_pancan_value() provide convenient interface to download multi-omics data from 3 databases by specifying one or several canonical datasets. It is derived from query_pancan_value() and support query for genomic signature. To query comprehensive datasets that UCSCXena supports, users can check UCSCXenaTools::XenaData and use get_pancan_value() directly.

Option opt_pancan is a nested list and allow to adjust the downloading details. For now, only cnv(toil),methylation(toil),miRNA(toil),miRNA(pcawg),promoter(pcawg) support optional parameters. The default set is .opt_pancan and we check meanings of sublist(parameters) through the following relationship.

"toil" database

1. mRNA–get_pancan_gene_value()

2. transcript–get_pancan_transcript_value()

3. protein–get_pancan_protein_value()

4. mutation–get_pancan_mutation_status()

5. cnv–get_pancan_cn_value()

6. methylation–get_pancan_methylation_value()

7. miRNA–get_pancan_miRNA_value()

"ccle" database

1. mRNA–get_ccle_gene_value()

2. protein–get_ccle_protein_value()

3. mutation–get_ccle_mutation_status()

4. cnv–get_ccle_cn_value()

"pcawg" database

1. mRNA–get_pcawg_gene_value()

2. miRNA–get_pcawg_miRNA_value()

3. promoter–get_pcawg_promoter_value()

4. fusion–get_pcawg_fusion_value()

5. APOBEC–get_pcawg_APOBEC_mutagenesis_value()

Examples

if (FALSE) { # \dontrun{
query_pancan_value("KRAS")
query_pancan_value("KRAS", database = "ccle")
query_pancan_value("KRAS", database = "pcawg")


query_pancan_value("ENSG00000000419",
  database = "pcawg",
  data_type = "fusion"
) # gene symbol also work

.opt_pancan

opt_pancan <- list(toil_cnv = list(use_thresholded_data = FALSE))
query_pancan_value("PTEN", data_type = "cnv", database = "toil", opt_pancan = opt_pancan)


opt_pancan <- list(toil_methylation = list(type = "450K", rule_out = "cg21115430", aggr = "Q25"))
query_pancan_value("PTEN", data_type = "methylation", database = "toil", opt_pancan = opt_pancan)
} # }