initPipeFrame {pipeFrame} | R Documentation |
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.
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")) )
defaultJobName |
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availableGenome |
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defaultCheckAndInstallFunc |
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defaultThreads |
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defaultTmpDir |
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defaultRefDir |
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defaultReference |
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No value will be returned.
initPipeFrame(availableGenome = c("hg19", "hg38", "mm9", "mm10"), defaultJobName = paste0("pkgname","-pipeline") )