importStructuralVariantsPURPLE: Import the somatic structural variants as estimated by GRIDSS...

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

Description

Import the somatic structural variants as estimated by GRIDSS / PURPLE.

Usage

importStructuralVariantsPURPLE(pathSV, passOnly = TRUE)

Arguments

pathSV	(character): Path to the <sample>.purple.sv.vcf.gz file containing the somatic structural variants as detected by GRIDSS / PURPLE.
passOnly	(logical): Only retain SV which were not found in the PON and/or were inferred by copy-number transition alone or any of the other filters.

Value

(GRanges) GRanges object containing the break-ends of the structural variants, so two rows for each SV (except when single break-end).

Author(s)

Job van Riet [e-mail]

See Also

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

Examples

	importStructuralVariantsPURPLE(pathSV = '<sample>.purple.sv.vcf.gz')

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