postAnalyseVEP: Runs VEP on a R and plot directory that superFreq has been...

View source: R/runVEP.R

postAnalyseVEPR Documentation

Runs VEP on a R and plot directory that superFreq has been run on.

Description

Runs VEP on a R and plot directory that superFreq has been run on.

Usage

postAnalyseVEP(
  outputDirectories,
  inputFiles = NA,
  metaData = NA,
  genome = "hg19",
  cpus = 1,
  cosmicDirectory = "",
  vepCall = "vep",
  forceRedo = F
)

Arguments

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.

Details

Runs VEP on the variants, and saves the variants (retrivable with loadData) with the addition information from VEP, and COSMIC if provided.


ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.