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

Usage

query_molecule_value(dataset, molecule, host = NULL)

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.

Value

a named vector.

Examples

# What does dense matrix mean?
table(UCSCXenaTools::XenaData$Type)
#> 
#> clinicalMatrix  genomicMatrix genomicSegment mutationVector 
#>            345            981            152            203 
# 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)
}