detectKataegis_OLD: Detect kataegis-like events by using a PCF algorithm.

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

Description

Uses piecewise constant fitting and additional hueristics to detect hypermutated (snvs) regions per chromosome.

Usage

detectKataegis_OLD(snv, min.snvs = 5, maxMeanDistance = 2000, maxk = 5)

Arguments

snv	(GRanges): GRanges object containing all SNV of a single sample.
min.snvs	(numeric): What is the minimum amount of SNV that a (constant fit) segment should have being calculated on. (How many SNV should have a consectutive fit)
maxMeanDistance	(numeric): The maximum mean interchromosomal distance segmented SNV.
maxk	(numeric): Max. amount of consecutive SNV which may be used to discover segmental breakpoints.

Value

(GRanges) A GRanges object containing all non-overlapping kataegis sites.

Author(s)

Job van Riet [e-mail]

See Also

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

Examples

# Example case.
detectKataegis(mutData, min.snvs = 5, maxMeanDistance = 1E3, maxk = 6)

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