importWGSOfSample: Imports all the WGS data of a single CPCT-02 sample.
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/helper_importWGSOfSample.R
Description
Imports all the WGS data of a single CPCT-02 sample.
Usage
1
importWGSOfSample(cpctId, inputFolder)
Arguments
cpctId
(character): Full CPCT identifier of sample, including the T suffix (used to find files).
inputFolder
(character): Path to the folder containing all WGS data of the sample (combinedData).
Details
Also runs CHORD for HRD predictions and ShatterSeek for chromothripsis samples.
Value
(list) List containing the WGS data of the sample.
Author(s)
Job van Riet j.vanriet@erasmusmc.nl
See Also
Other CPCT:
detectKataegis_OLD(),
findCPCTCenter(),
importLINXFusions(),
importPurityStatsPURPLE(),
importSomaticCopynumberPURPLE(),
importSomaticVariantsVEP(),
importStructuralVariantsPURPLE(),
importWGSOfCohort(),
importdriverCatalogHMF(),
performCHORD(),
performShatterSeek()
Examples
1
importWGSOfSample(cpctId = '<CPCTID>T', 'combinedData/')
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/helper_importWGSOfSample.R
Description
Imports all the WGS data of a single CPCT-02 sample.
Usage
1 | importWGSOfSample(cpctId, inputFolder)
|
Arguments
cpctId |
(character): Full CPCT identifier of sample, including the T suffix (used to find files). |
inputFolder |
(character): Path to the folder containing all WGS data of the sample (combinedData). |
Details
Also runs CHORD for HRD predictions and ShatterSeek for chromothripsis samples.
Value
(list) List containing the WGS data of the sample.
Author(s)
Job van Riet j.vanriet@erasmusmc.nl
See Also
Other CPCT:
detectKataegis_OLD(),
findCPCTCenter(),
importLINXFusions(),
importPurityStatsPURPLE(),
importSomaticCopynumberPURPLE(),
importSomaticVariantsVEP(),
importStructuralVariantsPURPLE(),
importWGSOfCohort(),
importdriverCatalogHMF(),
performCHORD(),
performShatterSeek()
Examples
1 | importWGSOfSample(cpctId = '<CPCTID>T', 'combinedData/')
|
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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