Changelog • biocohort

biocohort 0.1.1

Resubmission to CRAN. The package code is unchanged from 0.1.0; every change is in the documentation and the repository.

?biocohort names the three articles as vignette() calls instead of linking to them by a relative path that only exists on the website, and the package README links to the contributing guide by its full URL. CRAN’s pretest rejected 0.1.0 for both links.
The liftover_rtracklayer() example is wrapped in \donttest{}. Loading rtracklayer alone takes longer than the five seconds CRAN allows an example.
The Description field is rewritten in plainer sentences.
New examples for translate() on a cohort, translation_report(), load_analyses(), cohort_read(), register_liftover_backend(), register_ortholog_backend(), liftover_vcf(), and the Study, Subject, Cohort, AnalysisSpec, and TranslationResult constructors. The translation_report() example was a comment before, not code.
Help pages that still pointed to orthologize() now point to translate().
citation("biocohort") includes the Zenodo DOI.
README: install from r-universe as well as GitHub.
CI: a cran workflow runs the check the way CRAN’s pretest does.

First release. Earlier drafts carried the numbers 0.1.0 to 0.3.0 and were never tagged.

S7 classes Study, Subject, Cohort, and AnalysisSpec, built with study_new(), subject_new(), cohort_new(), and analysis_spec_new(). Each class validates on construction, including the raw Study(), Subject(), and Cohort() constructors.
validate_manifest() takes one long-format manifest (one row per sample, required columns subject_id, assay, sample_id, optional role plus subject-level columns) and returns subject_tbl, sample_map, and completeness_tbl. Species and assays are free-form values, never a fixed list and never columns. Every column is coerced to character, so a factor or a numeric column never breaks a downstream join.
validate_manifest(sample_cols = ) keeps named extra columns (fastq_1, fastq_2, lane, qc_status, and more) at the sample level instead of raising a false conflict.
read_manifest_csv() reads a manifest from CSV and delegates to validate_manifest().
validate_cohort() checks a Cohort for the four required sample_map columns, non-missing species, unique subject ids, and referential integrity.
sample_pairs() derives tumor and normal pairs from a sample_map on demand, with configurable role labels and a sep argument for the pair id.
example_cohort ships as a small demonstration dataset.

subjects(), samples(), and completeness() return plain tibbles read from a cohort. completeness(wide = TRUE) gives one row per subject and one column per assay.
subject() reads one subject from subject_tbl as a Subject object.
cohort_filter() keeps a subset of subjects or assays and returns a cohort that is still valid. drop_sample_ids removes specific sample ids instead of naming every sample to keep.
print() for Cohort, Subject, and AnalysisSpec shows subject and sample counts, extra sample columns, a QC summary, and registered analyses.

cohort_qc() flags or drops subjects or samples, recording the reason in qc_status/qc_reason columns (flag) or by removing the matching rows (drop). qc_log() reads the audit trail every call appends to cohort@qc, which is not cleared by cohort_filter(), so the record survives later structural changes to the cohort.

cohort_groups() groups a cohort’s subjects by one or more subject_tbl columns and returns one row per combination that actually occurs, with the matching subject ids. cohort_contrasts() enumerates every pairwise contrast between those groups, ready to pipe into cohort_filter() for each side.

cohort_derive() bins an existing numeric column at one or more named cutoffs and writes the result as a new column on subject_tbl or sample_map, so a cutoff like “early onset is 120 days or under” is a value passed in, not code. derive_log() reads the provenance every call appends to cohort@derived, which, like cohort@qc, is not cleared by cohort_filter().

read_manifest() reads a manifest from CSV, TSV, or Excel, always as text, and validates it in one call.
manifest_from_wide() reshapes a wide, one-row-per-subject table with one id column per assay into the long form validate_manifest() expects.
write_manifest() writes a cohort’s tables back out as one manifest. cohort_save() and cohort_read() keep a whole cohort as an RDS file.
read_study_yaml() builds a cohort from one YAML file that names the study, the manifest, the file paths, and the registered analyses. write_study_yaml() writes one back. Every path is resolved relative to the YAML file’s own directory.
apply_corrections() applies a table of documented overrides (level, id, column, value, reason) to a manifest before it is validated, and keeps an audit trail. read_corrections() reads that table from a file.

sample_sheet() writes the sample list a pipeline expects, with built-in templates for nf-core/rnaseq, nf-core/rnavar, nf-core/atacseq, and nf-core/sarek. sample_sheet_templates() lists the built-in names.
check_paths() tests that the file paths named in cohort@paths and in known sample-level path columns exist, without ever raising an error.
as_coldata() returns a Cohort’s per-sample metadata as row-named data, ready for a SummarizedExperiment’s colData. join_metadata() carries that metadata into a SummarizedExperiment, a Seurat object, or a plain data frame.
project_root(), project_path(), ensure_dir(), and read_dotenv() find a project’s root folder, build paths under it, and read a .env file.

analysis_register(), analysis_list(), and analysis_spec() manage AnalysisSpec entries in a cohort. format, reader, and key_cols default from the spec’s path_template and level when not given.
load_analysis() and load_analyses() resolve a spec’s path_template per subject, per pair, or per cohort, read the files with the spec’s reader, and record which files were found. Subject and pair units are enumerated only for the spec’s own assay. analysis_files() returns that record.
A path_template ending in .parquet now gets arrow::read_parquet as its default reader, the same way .csv, .tsv, .txt, and .rds already do.

translate() moves a feature table across genome builds or species. Coordinate features go through a liftover backend; gene features go through an ortholog backend. orthologize() still works as an alias and warns once per session. translation_report() returns the per-analysis results.
For a whole cohort, the source species is inferred from subject_tbl when every subject shares one species. A cohort with more than one species is split by species, translated, and recombined, as long as the analysis table carries a subject_id column.
liftover_intervals() with an rtracklayer backend and a crossmap backend, plus liftover_vcf() for allele-aware variant liftover through CrossMap. Backends are registered with register_liftover_backend().
ortholog_genes() with an offline babelgene backend, registered with register_ortholog_backend(). Model-to-model pairs pivot through human. The backend accepts a cache file so repeated lookups skip babelgene.
TranslationResult keeps mapped and unmapped features under one .feature_id key, for both coordinate and gene features. translation_stats() summarizes them.

Formatting with air, hooks with prek, lintr config, and CI on pull requests into dev and main.