assign_study_data_types: Summarize data types for the study

In nf-osi/nfportalutils: NF Portal Utilities

Summarize data types for the study

Description

Data types are summarized, or "rolled-up", for the study based on its child file annotations. Summary values are added back as and overwrites the current dataType annotation for the study. See also the related update_study_annotations, where study-level annotations are rolled down to child files. Note that under-the-hood this now wraps a generalized util summarize_attribute.

Usage

assign_study_data_types(
  study_table_id,
  fileview_id,
  id_col = "studyId",
  attribute = "dataType",
  dry_run = TRUE
)

Arguments

study_table_id	Synapse ID of reference portal study table. Used to get study ids.
fileview_id	Synapse ID of the reference portal fileview.
id_col	Name of the study id column in study_table_id and fileview_id. Defaults to studyId.
attribute	Attribute being summarized using fileview. Defaults to dataType.
dry_run	Default = TRUE. Whether to update as well or just return list of annotation objects.

Value

List of annotations objects.

Examples

## Not run: 
assign_study_data_types(study_table_id = 'syn52694652',
                        fileview_id = 'syn16858331',
                        id_col = 'studyId',
                        attribute = 'dataType',
                        dry_run = T)

## End(Not run)

nf-osi/nfportalutils documentation built on Feb. 26, 2024, 1:05 p.m.