initPipeFrame {pipeFrame}R Documentation

initialize the pipeFrame package

Description

This function should be called first in R terminal for general users. And it should be used in .onLoad() function for package developers. In this function, several parameters need to be defined and configured, including genome, job name, reference directory, temporary directory, check and install function, threads number, reference list, etc.

Usage

initPipeFrame(
  defaultJobName,
  availableGenome = c("hg19", "hg38", "mm9", "mm10", "danRer10", "galGal5", "galGal4",
    "rheMac3", "rheMac8", "panTro4", "rn5", "rn6", "sacCer2", "sacCer3", "susScr3",
    "testgenome"),
  defaultCheckAndInstallFunc = NULL,
  defaultThreads = 2,
  defaultTmpDir = getwd(),
  defaultRefDir = file.path(getwd(), "refdir"),
  defaultReference = list(test = list(file = "fileName", rc = "obj"))
)

Arguments

defaultJobName

Character scalar. The default job name for the package. When users use pipeFrame package, defaultJobName is "pipeFrame-pipeline".

availableGenome

Character scalar or vector. Configure the available valid genome such as "hg19", "mm10", etc.

defaultCheckAndInstallFunc

Function scalar. The function needs to call runWithFinishCheck

defaultThreads

Numeric scalar. The maximum thread limit for each step. Default:2

defaultTmpDir

Character scalar. The directory of intermediate results for all steps. Default: Current working directory.

defaultRefDir

Character scalar. The directory of reference data. Default: file.path(getwd(),"refdir")

defaultReference

List scalar. List of reference files.

Value

No value will be returned.

Examples

initPipeFrame(availableGenome = c("hg19", "hg38", "mm9", "mm10"),
              defaultJobName = paste0("pkgname","-pipeline")
)


[Package pipeFrame version 1.10.0 Index]