Package 'biscuiteerData'

Supplementary Datasets for Biscuiteer

Description

A handful of datasets to be used in biscuiteer

Author(s)

Timothy J Triche Jr [email protected],

Wanding Zhou [email protected],

Ben Johnson [email protected],

Jacob Morrison [email protected],

Lyong Heo [email protected]

See Also

Useful links:

• https://github.com/trichelab/biscuiteer

• Report bugs at https://github.com/trichelab/biscuiteer/issues

Examples

Zhou_solo_WCGW_inCommonPMDs.hg19 <-
      biscuiteerDataGet("Zhou_solo_WCGW_inCommonPMDs.hg19.rda")
  PMDs.hg19 <- biscuiteerDataGet("PMDs.hg19.rda")

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Cache all biscuiteer data

Description

Cache all biscuiteer data

Usage

biscuiteerDataCacheAll(dateAdded = "all", showProgress = FALSE)

Arguments

dateAdded	Version of the data (given by the date added), if "all" then all dates will be cached (DEFAULT: "all")
showProgress	Whether to show progress of download (DEFAULT: FALSE)

Value

         TRUE

Examples

biscuiteerDataCacheAll()

---

Retrieve biscuiteer data

Description

Retrieve biscuiteer data

Usage

biscuiteerDataGet(title, dateAdded = "2019-09-25", verbose = FALSE)

Arguments

title	Title of the data
dateAdded	Version of the data (given by the date added) (DEFAULT: "2019-09-25")
verbose	Whether to output ExperimentHub message (DEFAULT: FALSE)

Value

      Data object

Examples

wcgws <- biscuiteerDataGet("Zhou_solo_WCGW_inCommonPMDs.hg19.rda")

---

List all biscuiteer data

Description

List all biscuiteer data

Usage

biscuiteerDataList(dateAdded = "all")

Arguments

dateAdded

Version of the data (given by the date added), if "all" then all dates will be shown (DEFAULT: "all")

Value

     All titles from biscuiteer data

Examples

biscuiteerDataList()

---

List all versions of biscuiteer data

Description

List all versions of biscuiteer data

Usage

biscuiteerDataListDates()

Value

Sorted unique dates in biscuiteer data

Examples

biscuiteerDataListDates()

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PMDs.hg19

Description

Common PMD locations in hg19 genome

Details

Source URL: http://zwdzwd.io/pmd/PMD_coordinates_hg19.bed.gz Source type: BED file Return type: GRanges

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PMDs.hg38

Description

Common PMD locations in hg38 genome

Details

Source URL: http://zwdzwd.io/pmd/PMD_coordinates_hg38.bed.gz Source type: BED file Return type: GRanges

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Zhou_solo_WCGW_inCommonPMDs.hg19

Description

Solo WCGWs living in hg19 common PMDs

Details

Source URL: http://zwdzwd.io/pmd/solo_WCGW_inCommonPMDs_hg19.bed.gz Source type: BED file Return type: GRanges

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Zhou_solo_WCGW_inCommonPMDs.hg38

Description

Solo WCGWs living in hg38 common PMDs

Details

Source URL: http://zwdzwd.io/pmd/solo_WCGW_inCommonPMDs_hg38.bed.gz Source type: BED file Return type: GRanges

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