curatedTCGAData-helpers {TCGAutils} | R Documentation |
Additional helper functions for cleaning and uncovering metadata
within a downloaded MultiAssayExperiment
from curatedTCGAData
.
The getSubtypeMap
function provides a 2 column data.frame
with in-data variable names and an interpreted names. The
getClinicalNames
function provides a vector of variable names that
exist in the colData
slot of a downloaded MultiAssayExperiment
object. These variables are obtained from
getFirehoseData by default and tend to be present
across most cancer codes.
getSubtypeMap(multiassayexperiment) getClinicalNames(diseaseCode) splitAssays(multiassayexperiment, sampleCodes = c("01", "11")) sampleTables(multiassayexperiment, vial = FALSE)
multiassayexperiment |
A MultiAssayExperiment object |
diseaseCode |
A TCGA cancer code (e.g., "BRCA") |
sampleCodes |
A string of sample type codes
(refer to |
vial |
(logical default FALSE) whether to display vials in the table output |
getSubtypeMap: A data.frame
with columns representing
actual data variables and explanatory names
getClinicalNames: A vector
of names that correspond to
a particular disease code.
Separates samples by indicated sample codes into different assays
in a MultiAssayExperiment
. Refer to the sampleTypes
data object for a list of available codes. This operation generates
n times the number of assays based on the number of sample codes
entered. By default, primary solid tumors ("01") and solid tissue
normals ("11") are seperated out.
Display all the available samples in each of the assays
## Not run: library(curatedTCGAData) coad <- curatedTCGAData(diseaseCode = "COAD", assays = "CNA*", dry.run = FALSE) getSubtypeMap(coad) ## End(Not run) getClinicalNames("COAD")