getDatasets {InterMineR} | R Documentation |
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 Service object containing the base URL and API token, created by |
type |
a character string defining the type of feature for which the information about the available datasets will be retrieved. Use the |
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 |
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
# 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" )