dataHub-class: dataHub Class

In rworkflow/ReUseData: Reusable and reproducible Data Management

dataHub Class

Description

dataHub class, constructor, and methods.

Usage

dataHub(BFC)

dataHub(BFC)

## S4 method for signature 'dataHub'
show(object)

dataNames(object)

dataParams(object)

dataNotes(object)

dataPaths(object)

dataYml(object)

dataTags(object)

## S4 method for signature 'dataHub'
dataTags(object)

dataTags(object, append = TRUE) <- value

## S4 replacement method for signature 'dataHub'
dataTags(object, append = FALSE) <- value

## S4 method for signature 'dataHub,ANY,ANY,ANY'
x[i, j, drop]

## S4 replacement method for signature 'dataHub,ANY,ANY,ANY'
x[i, j] <- value

## S4 method for signature 'dataHub'
c(x, ...)

toList(
  x,
  listNames = NULL,
  format = c("list", "json", "yaml"),
  type = NULL,
  file = character()
)

Arguments

BFC	A BiocFileCache object created for data and recipes.
object	A dataHub object.
append	Whether to append new tag or replace all tags.
value	A dataHub object
x	A dataHub object.
i	The integer index of the dataHub object, or a logical vector same length as the dataHub object.
j	inherited from [ generic.
drop	Inherited from [ generic.
...	More dataHub objects to combine.
listNames	A vector of names for the output list.
format	can be "list", "json" or "yaml". Supports partial match. Default is list.
type	The type of workflow input list, such as cwl.
file	The file name to save the data list in required format. The data extension needs to be included, e.g., ".json" or ".yml".

Value

dataHub: a dataHub object.

dataNames: the names of datasets in dataHub object.

dataParams: the data recipe parameter values for datasets in dataHub object.

dataNotes: the notes of datasets in dataHub object.

dataPaths: the file paths of datasets in dataHub object.

dataYml: the yaml file paths of datasets in dataHub object.

dataTags: the tags of datasets in dataHub object.

toList: A list of datasets in specific format, and a file if file argument is specified.

Examples

outdir <- file.path(tempdir(), "SharedData")
dataUpdate(outdir, cloud = TRUE)
dd <- dataSearch(c("liftover", "GRCh38"))
dataNames(dd)
dataParams(dd)
dataNotes(dd)
dataTags(dd)
dataYml(dd)
toList(dd)
toList(dd, format = "yaml")
toList(dd, format = "json", file = tempfile())

rworkflow/ReUseData documentation built on Dec. 7, 2023, 11 p.m.