configureValue {esATAC} | R Documentation |
These functions are used to configure and query global parameters. The items include "threads","tmpdir","refdir","genome","knownGene", "bsgenome","bt2Idx","DHS" and "blacklist". "threads","tmpdir","refdir","genome" are setable and getable. While the others are readable only. You should consider to configure these parameters before starting the workflow.
For get getConfigure
and setConfigure
:
Character
scalar, the path for reference data being installed to and storage.
Character
scalar, the genome(like hg19, mm10, etc.) reference data in "refdir" to be used in the pipeline.
Character
scalar, the temporary file storage path
Integer
scalar, the max threads allowed to be created
For get getConfigure
only:
TxDb
scalar, known gene TxDb object
BSGenome
scalar, BSGenome object
Character
scalar, bowtie2 index path prefix
Character
scalar, DHS BED file path
Character
scalar, blacklist BED file path
getAllConfigure() getConfigure(item = c("threads", "tmpdir", "refdir", "genome", "knownGene", "bsgenome", "annoDb", "bt2Idx", "DHS", "blacklist", "SNP")) setConfigure(item = c("threads", "tmpdir", "refdir", "genome"), val)
item |
|
val |
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Character
scalar for getting
"tmpdir","refdir", bt2Idx","DHS" and "blacklist",
all of them are file or directory path.
Getting "genome" will return the genome tag like "hg19" "mm10" etc.
Integer
scalar for getting "threads",
the max threads can be created by the process.
TxDb
object for getting "knownGene".
BSGenome
object for getting "bsgenome"
Zheng Wei
getAllConfigure() getConfigure("threads") options(atacConf=setConfigure("tmpdir",tempdir()))