UCSCXenaShiny (version 2.1.0)

query_molecule_value: Get Molecule or Signature Data Values from Dense (Genomic) Matrix Dataset of UCSC Xena Data Hubs

Description

Get Molecule or Signature Data Values from Dense (Genomic) Matrix Dataset of UCSC Xena Data Hubs

Usage

query_molecule_value(dataset, molecule, host = NULL)

Value

a named vector.

Arguments

dataset

a UCSC Xena dataset in dense matrix format (rows are features (e.g., gene, cell line) and columns are samples).

molecule

a molecular identifier (e.g., "TP53") or a formula specifying genomic signature ("TP53 + 2 * KRAS - 1.3 * PTEN"). NOTE, when a signature is specified, a space must exist in the input.

host

a UCSC Xena host, default is NULL, auto-detect from the dataset.

Examples

# What does dense matrix mean?
table(UCSCXenaTools::XenaData$Type)
# It is a the UCSC Xena dataset with "Type" equals to "genomicMatrix"
if (FALSE) {
dataset <- "ccle/CCLE_copynumber_byGene_2013-12-03"
x <- query_molecule_value(dataset, "TP53")
head(x)

signature <- "TP53 + 2*KRAS - 1.3*PTEN" # a space must exist in the string
y <- query_molecule_value(dataset, signature)
head(y)
}