| Title: | Access the Antibodyome Atlas of Autoantibody Profiling Datasets |
|---|---|
| Description: | Client for the antibodyome-atlas, a curated catalog of autoantibody profiling datasets and papers (protein/antigen microarrays and related platforms) drawn from public repositories such as GEO and ArrayExpress. Metadata is fetched live from the atlas's GitHub-hosted JSON manifest, so results always reflect the latest curated data (or a pinned release, for reproducibility). Provides functions to list and filter datasets, resolve citations and related records, and download the underlying data files. |
| Authors: | Alexandre Marques [aut, cre] |
| Maintainer: | Alexandre Marques <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.1.0 |
| Built: | 2026-10-19 14:01:46 UTC |
| Source: | https://github.com/ahcm088/antibodyome-atlas |
Get the citation for a dataset, ready to paste into a manuscript
aab_citation(atlas_id, ref = "main")aab_citation(atlas_id, ref = "main")
atlas_id |
An atlas id, e.g. '"AAB-000004"'. |
ref |
Git ref (branch, tag, or commit SHA) to read from. Defaults to '"main"' (the latest curated data). Pin to a release tag (e.g. '"v1.0.0"') for reproducible results in a publication. |
A one-row [tibble::tibble()] with columns 'atlas_id', 'dataset_link', 'citation', 'doi', 'pubmed_link', 'publisher_link'. Any publication field is 'NA' if the record has no associated publication.
## Not run: aab_citation("AAB-000004") ## End(Not run)## Not run: aab_citation("AAB-000004") ## End(Not run)
Get a single dataset record, with its publication and platforms resolved
aab_dataset(atlas_id, ref = "main")aab_dataset(atlas_id, ref = "main")
atlas_id |
An atlas id, e.g. '"AAB-000004"'. |
ref |
Git ref (branch, tag, or commit SHA) to read from. Defaults to '"main"' (the latest curated data). Pin to a release tag (e.g. '"v1.0.0"') for reproducible results in a publication. |
A list with the dataset's fields plus two resolved fields: 'publication' (a one-row tibble, or 'NULL' if none) and 'platforms_detail' (a tibble joining 'platforms[].platform_id' from the dataset onto 'aab_platforms()', keeping 'n_proteins_reported').
## Not run: aab_dataset("AAB-000004") ## End(Not run)## Not run: aab_dataset("AAB-000004") ## End(Not run)
List all datasets/papers in the atlas
aab_datasets(ref = "main")aab_datasets(ref = "main")
ref |
Git ref (branch, tag, or commit SHA) to read from. Defaults to '"main"' (the latest curated data). Pin to a release tag (e.g. '"v1.0.0"') for reproducible results in a publication. |
A [tibble::tibble()], one row per record, with columns matching 'schema/dataset.schema.json' ('atlas_id', 'record_type', 'title', 'organism', 'conditions', 'total_sample_n', 'platforms', 'dataset_link', 'curated_availability', etc.). List-valued fields come back as list-columns.
## Not run: ds <- aab_datasets() ds[ds$record_type == "DATASET", c("atlas_id", "title")] ## End(Not run)## Not run: ds <- aab_datasets() ds[ds$record_type == "DATASET", c("atlas_id", "title")] ## End(Not run)
Downloads whatever is at the record's 'dataset_link'. For records with 'record_type == "DATASET"' this is usually a repository landing page (e.g. a GEO accession page) rather than a direct file: check 'curated_availability' first, and note that some repositories require navigating from that page to the actual supplementary files by hand.
aab_download(atlas_id, destdir = tempdir(), destfile = NULL, ref = "main")aab_download(atlas_id, destdir = tempdir(), destfile = NULL, ref = "main")
atlas_id |
An atlas id, e.g. '"AAB-000004"'. |
destdir |
Directory to save the file into. Defaults to a temp dir. |
destfile |
File name to save as. Defaults to the last path segment of 'dataset_link'. |
ref |
Git ref (branch, tag, or commit SHA) to read from. Defaults to '"main"' (the latest curated data). Pin to a release tag (e.g. '"v1.0.0"') for reproducible results in a publication. |
The local file path, invisibly.
## Not run: aab_download("AAB-000004") ## End(Not run)## Not run: aab_download("AAB-000004") ## End(Not run)
List the link-reachability check history
aab_link_status(ref = "main")aab_link_status(ref = "main")
ref |
Git ref (branch, tag, or commit SHA) to read from. Defaults to '"main"' (the latest curated data). Pin to a release tag (e.g. '"v1.0.0"') for reproducible results in a publication. |
A [tibble::tibble()] with one row per automated check, appended over time by the atlas's scheduled link checker — see ‘checked_at'/'reachable' to see whether a given dataset’s link has gone stale.
List all assay platforms referenced by atlas datasets
aab_platforms(ref = "main")aab_platforms(ref = "main")
ref |
Git ref (branch, tag, or commit SHA) to read from. Defaults to '"main"' (the latest curated data). Pin to a release tag (e.g. '"v1.0.0"') for reproducible results in a publication. |
A [tibble::tibble()] with columns 'platform_id', 'name', 'technology'. Per-study protein/feature counts live on the dataset record ('aab_datasets()$platforms'), not here — see 'schema/README.md' in the atlas repo for why.
List all publications referenced by atlas datasets
aab_publications(ref = "main")aab_publications(ref = "main")
ref |
Git ref (branch, tag, or commit SHA) to read from. Defaults to '"main"' (the latest curated data). Pin to a release tag (e.g. '"v1.0.0"') for reproducible results in a publication. |
A [tibble::tibble()] with columns 'publication_id', 'citation', 'doi', 'pubmed_link', 'publisher_link'.