importSomaticCopynumberPURPLE: Import the somatic CNV segments as estimated by PURPLE.
In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
View source: R/import_somaticCopynumbersPURPLE.R
Description
Import the somatic CNV segments as estimated by PURPLE.
Usage
1
importSomaticCopynumberPURPLE(pathCNV)
Arguments
pathCNV
(character): Path to the <sample>.purple.cnv.somatic.tsv file containing the somatic CNV regions as detected by PURPLE.
Details
Will also convert the absolute copynumbers into CN-States for downstream analysis.
Value
(GRanges) GRanges object containing the somatic variants and assorted annotations.
Author(s)
Job van Riet j.vanriet@erasmusmc.nl
See Also
Other CPCT:
detectKataegis_OLD(),
findCPCTCenter(),
importLINXFusions(),
importPurityStatsPURPLE(),
importSomaticVariantsVEP(),
importStructuralVariantsPURPLE(),
importWGSOfCohort(),
importWGSOfSample(),
importdriverCatalogHMF(),
performCHORD(),
performShatterSeek()
Examples
1
importSomaticCopynumberPURPLE(pathCNV = '<sample>.purple.cnv.somatic.tsv')
J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/import_somaticCopynumbersPURPLE.R
Description
Import the somatic CNV segments as estimated by PURPLE.
Usage
1 | importSomaticCopynumberPURPLE(pathCNV)
|
Arguments
pathCNV |
(character): Path to the <sample>.purple.cnv.somatic.tsv file containing the somatic CNV regions as detected by PURPLE. |
Details
Will also convert the absolute copynumbers into CN-States for downstream analysis.
Value
(GRanges) GRanges object containing the somatic variants and assorted annotations.
Author(s)
Job van Riet j.vanriet@erasmusmc.nl
See Also
Other CPCT:
detectKataegis_OLD(),
findCPCTCenter(),
importLINXFusions(),
importPurityStatsPURPLE(),
importSomaticVariantsVEP(),
importStructuralVariantsPURPLE(),
importWGSOfCohort(),
importWGSOfSample(),
importdriverCatalogHMF(),
performCHORD(),
performShatterSeek()
Examples
1 | importSomaticCopynumberPURPLE(pathCNV = '<sample>.purple.cnv.somatic.tsv')
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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