postAnalyseVEP | R Documentation |
Runs VEP on a R and plot directory that superFreq has been run on.
postAnalyseVEP(
outputDirectories,
inputFiles = NA,
metaData = NA,
genome = "hg19",
cpus = 1,
cosmicDirectory = "",
vepCall = "vep",
forceRedo = F
)
outputDirectories |
named list with Rdirectory and plotDirectory. |
inputFiles |
named list as in analyse. |
genome |
character: such as 'hg19', 'hg38' or 'mm10' |
cpus |
integer. maximum number of parallel threads. |
cosmicDirectory |
character: path to COSMIC directory. (optional) |
forceRedo |
boolean: if TRUE, previously saved data is ignored and overwritten. |
Runs VEP on the variants, and saves the variants (retrivable with loadData) with the addition information from VEP, and COSMIC if provided.
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