opal.annotate {opalr} | R Documentation |
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.datasources()
,
opal.datasource()
,
opal.tables()
,
opal.table()
,
opal.valueset()
,
opal.variable_summary()
,
opal.variables()
,
opal.variable()
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)
[Package opalr version 3.4.1 Index]