getDatasets: Retrieve information about the available datasets of a Mine...
In InterMineR: R Interface with InterMine-Powered Databases

Description Usage Arguments Details Value Author(s) See Also Examples

This function retrieves information about the available datasets of a mine instance. It is necessary to specify the type of feature (e.g. Gene, TFBindingSite) for this mine, and a value of this feature OR of one of its child_name values.

getDatasets(
  im, 
  type,                      
  child_name,    
  value,
  op
)

`im`	a list containing the base URL and API token.
`type`	a character string defining the type of feature for which the information about the available datasets will be retrieved. Use the `listDatasets` function to retrieve types with available datasets on each mine.
`child_name`	a character string defining the child_name values of type, which will be used to retrieve the information about the available datasets. Use `getModel` function to retrieve the available child_name values for each type.
`value`	a character string defining the value of the child_name.
`op`	a character string defining the op argument.

The getDatasets function uses an InterMineR query to retrieve the information of the available datasets for:

1. a specific mine (e.g. FlyMine)

2. a specific type of feature (e.g. Gene, TFBindingSite) for this mine, and

3. a specific value of this feature OR of one of its child_name values.

For all genes of Drosophila melanogaster (Gene.organism = Drosophila melanogaster) OR for a specific gene (Gene LOOKUP PPARG)

a data.frame containing information about about the available datasets for a specific type of feature (e.g. Gene) on a specific mine instance (HumanMine, FlyMine, etc.).

InterMine Team

listDatasets, getModel

# Define mines
im.fly = initInterMine(listMines()["FlyMine"])
im.human = initInterMine(listMines()["HumanMine"])

# get information about all available datasets of Drosophila melanogaster genes
dme_gene_datasets = getDatasets(
  im = im.fly,
  type = "Gene",
  child_name = "organism.name",
  value = "Drosophila melanogaster",
  op = "="
)

# get available datasets for PPARG gene from FlyMine
pparg_related = getDatasets(
  im = im.fly,
  type = "Gene",
  value = "PPARG",
  op = "LOOKUP"
)

# get available datasets for PPARG gene from HumanMine
pparg_related.2 = getDatasets(
  im = im.human,
  type = "Gene",
  value = "PPARG",
  op = "LOOKUP"
)