query_molecule_value: Get Molecule or Signature Data Values from Dense (Genomic)...

Description Usage Arguments Value Examples

View source: R/query_value.R

Description

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

Usage

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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

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# What does dense matrix mean?
table(UCSCXenaTools::XenaData$Type)
# It is a the UCSC Xena dataset with "Type" equals to "genomicMatrix"
## Not run: 
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)

## End(Not run)

UCSCXenaShiny documentation built on Nov. 29, 2021, 9:06 a.m.