performLINX: Run LINX on one or multiple samples to discover fusion and...

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

For installation instructions, please see the 'howToInstallLINX' vignette. It will output the (relevant) files in the combinedData/ folder.

Usage

performLINX(
  pathCombined,
  cpctIds,
  nThreads,
  dryRun = TRUE,
  pathLINX = "/mnt/onco0002/repository/software/LINX_v1.16/"
)

Arguments

pathCombined	(character): Path to the combinedData/ folder containing the symlinks to the WGS files of the data-request (DR).
cpctIds	(character): The samples which will be retrieved.
nThreads	(integer): Number of cores to run multiple LINX in parallel.
dryRun	(logical): Only output the tmp. file which stores the commands (TRUE) or run the commands (FALSE).
pathLINX	(character): Path to the folder containing LINX and the respective databases.

Value

(NULL) Does not return anything, only outputs logging messages.

Examples

 runLINX('DR-071/combinedData/', c('CPCT02124567', 'CPCT02012345123'), nThreads = 10)

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.