runVEP: Run VEP on the provided variants
In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.
runVEP R Documentation
Run VEP on the provided variants
Description
Run VEP on the provided variants
Usage
runVEP(
variants,
plotDir,
cpus = 1,
genome = "hg19",
vepCall = "vep",
forceRedoVEP = F,
rareGermline = T
)
Arguments
variants
variants: The variants to be VEPed.
plotDir
character: The plot directory where outputSomatics have been run.
cpus
integer: The number of cpus to be used as most.
forceRedoVEP
Logical: if VEP should be rerun even if saved data already exists.
Details
This function calls VEP on the output from outputSomaticVariants. For this, VEP needs to be callable by system('vep').
ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.
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| runVEP | R Documentation |
Run VEP on the provided variants
Description
Run VEP on the provided variants
Usage
runVEP(
variants,
plotDir,
cpus = 1,
genome = "hg19",
vepCall = "vep",
forceRedoVEP = F,
rareGermline = T
)
Arguments
variants |
variants: The variants to be VEPed. |
plotDir |
character: The plot directory where outputSomatics have been run. |
cpus |
integer: The number of cpus to be used as most. |
forceRedoVEP |
Logical: if VEP should be rerun even if saved data already exists. |
Details
This function calls VEP on the output from outputSomaticVariants. For this, VEP needs to be callable by system('vep').
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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