importWGSOfCohort: Imports all the WGS data of multiple samples (cohort).

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

Imports all the WGS data of multiple samples (cohort).

Usage

importWGSOfCohort(
  cpctIds,
  inputFolder,
  nThreads = 1,
  performAggregation = TRUE
)

Arguments

cpctIds	(character): Full CPCT identifiers of samples, including the T suffixes (used to find files).
inputFolder	(character): Path to the folder containing all WGS data of the samples (combinedData).
nThreads	(integer): Number of threads to use; default is 1.
performAggregation	(logical): Should aggregation be performed? (Is needed for further processing)

Value

(list) List containing the aggregated WGS data of the underlying samples.

Author(s)

Job van Riet [e-mail]

See Also

Other CPCT: detectKataegis_OLD(), findCPCTCenter(), importLINXFusions(), importPurityStatsPURPLE(), importSomaticCopynumberPURPLE(), importSomaticVariantsVEP(), importStructuralVariantsPURPLE(), importWGSOfSample(), importdriverCatalogHMF(), performCHORD(), performShatterSeek()

Examples

	importWGSOfCohort(cpctId = '<CPCTIDs>', 'combinedData/')

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.