AnVIL Package Tools
AnVIL
The AnVIL package provides binary package installation, utitlities for manipulating table and data resources, and functions for moving files between AnVIL Terra and Google cloud storage. It also provides programmatic access with helper functions to the Terra, Leonardo, Rawls, Dockstore, and Gen3 RESTful programming interface. For more information, see
AnVILPublish
Create and update AnVIL workspaces from R / Bioconductor packages. For more information, see
Metadata access and overview
AnVIL package tools can be used to discover incompatibilities or ambiguities in study annotation. BJ’s class worked through metadata survey exercises. An example of incompatible/ambiguous annotation is present in the Autism workspaces.
Workspace showing an example of incompatible/ambiguous annotation in Autism workspaces
We are looking at two studies from NYGC referring to autism, one has substring ACE2 and the other SSC. What we see above is that AFFECTION_STATUS is coded 1/2 in the SSC study, and more prosaically in the ACE2 study. It may be that the labels in ACE2 study are more problematic as the options seem to be “0”, “ASD affected”, “ASD Affected”, and “Diagnosis uncertain” – or perhaps it is just a letter casing issue.
The ingestion group was notified and replied that “there is no process for the AnVIL team to retrospectively address existing data”. Interest was expressed in learning more about our metadata survey capabilities.