opal.annotate: Apply the annotations to a Opal table

In opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils

Apply the annotations to a Opal table

Description

Set the provided annotations (as the one that can be retrieved from opal.annotations) to the table's data dictionary. Variables that do not exists in the table are ignored.

Usage

opal.annotate(opal, datasource, table, annotations)

Arguments

opal	Opal object.
datasource	Name of the datasource.
table	Name of the table in the datasource.
annotations	A data frame of annotations, with the expected columns: 'variable' (variable name), 'taxonomy' (the taxonomy name), 'vocabulary' (the vocabulary name) and 'term' (the term value, if NULL of NA the annotation is removed).

See Also

Other datasource functions: opal.annotations(), opal.attribute_values(), opal.datasource(), opal.datasources(), opal.table(), opal.tables(), opal.valueset(), opal.variable(), opal.variable_summary(), opal.variables()

Examples

## Not run: 
o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
opal.logout(o)

## End(Not run)

opalr documentation built on Sept. 18, 2024, 9:11 a.m.