Global parameters configure

Description

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:

"refdir"

Character scalar, the path for reference data being installed to and storage.

"genome"

Character scalar, the genome(like hg19, mm10, etc.) reference data in "refdir" to be used in the pipeline.

"tmpdir"

Character scalar, the temporary file storage path

"threads"

Integer scalar, the max threads allowed to be created

For get getConfigure only:

"knownGene"

TxDb scalar, known gene TxDb object

"bsgenome"

BSGenome scalar, BSGenome object

"bt2Idx"

Character scalar, bowtie2 index path prefix

"DHS"

Character scalar, DHS BED file path

"blacklist"

Character scalar, blacklist BED file path

Usage

getAllConfigure()

getConfigure(item = c("threads", "tmpdir", "refdir", "genome", "knownGene",
  "bsgenome", "annoDb", "bt2Idx", "DHS", "blacklist", "SNP"))

setConfigure(item = c("threads", "tmpdir", "refdir", "genome"), val)

Arguments

Value

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"

Author(s)

Zheng Wei

See Also

atacSamToBed atacBedUtils

Examples

getAllConfigure()

getConfigure("threads")

options(atacConf=setConfigure("tmpdir",tempdir()))