num_specimens: Get number of specimens

In Sage-Bionetworks/dccmonitor: Monitor Data Validation

Get number of specimens

Description

Get the number of unique specimens for a study from the metadata files. Checks for ids in the manifest, biospecimen metadata, and assay metadata.

Usage

num_specimens(study_view, meta_types = c("manifest", "biospecimen", "assay"))

Arguments

study_view	The file view for a study, with the columns 'file_data', where each element is a tibble with the data, and metadataType, where each element is the metadataType for the file.
meta_types	List of metadata types to gather ids from. Default is 'manifest', 'assay', and 'biospecimen'.

Value

Number of unique specimen ids or 0 if no metadataTypes manifest, biospecimen, assay exist in 'study_view'.

Sage-Bionetworks/dccmonitor documentation built on May 28, 2022, 10:39 a.m.