getDatasets: Retrieve information about the available datasets of a Mine...

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

View source: R/getDatasets.R

Description

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.

Usage

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

Arguments

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.

Details

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)

Value

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.).

Author(s)

InterMine Team

See Also

listDatasets, getModel

Examples

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# 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"
)

InterMineR documentation built on Dec. 7, 2018, 6 p.m.