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This glossary defines the terms used across biocohort’s documentation and code.
| Term | Definition |
|---|---|
| Subject | One organism in a study. Each subject has a unique
subject_id and metadata such as species, genotype, or
cohort. A row in subject_tbl. |
| Species | The species of a subject, for example “rat”, “mouse”, or “human”. Species are free-form values, not a fixed list, and are stored lower case. Required in subject metadata. |
| Cohort | A group of subjects analyzed together. It combines subject-level metadata, sample-to-assay mappings, and optional study context. The main data container in biocohort. |
| Study | Project-level metadata: study ID, title, hypotheses, aims, assay types, and genome build versions. Optional context for a cohort. |
| Term | Definition |
|---|---|
| Sample | A biospecimen (tissue or cells) collected from a subject for an assay. Samples have a unique ID, for example a tumor or normal sample. |
| Assay | A molecular technique applied to a sample. Assays are free-form
values, not a fixed list, for example wgs,
wes, atac, bulk_rna,
scrna. A new assay is just a new label in the
assay column. |
Role (role) |
The part a sample plays within its assay, for example
"tumor" or "normal". A design with no
tumor/normal split can leave role as NA. |
| Tumor sample | A sample from tumor tissue or neoplastic cells: a
sample_map row with role = "tumor". |
| Normal sample | A sample from non-neoplastic tissue or a control: a
sample_map row with role = "normal". A
baseline for somatic mutation calling. |
Sample ID (sample_id) |
A unique ID for one sample, separate from the subject ID. Tells apart samples from the same subject. |
Pair (pair_id) |
A tumor and normal pairing of two samples of the same assay, for one
subject. Derived on demand from sample_map with
sample_pairs(). The pair_id is
paste0(tumor_sample_id, "__", normal_sample_id). Pairing
works for any assay and is not stored in sample_map
itself. |
| Table | Purpose | Common columns |
|---|---|---|
| subject_tbl | Subject-level metadata, one row per subject. | subject_id, species, sex,
strain, genotype, cohort,
timepoint, notes |
| sample_map | The long-format map of subjects to samples, one row per sample. A new assay is a new row, never a new column. | subject_id, assay, sample_id,
role |
| completeness_tbl | Sample counts per assay, one row per subject_id and
assay pair. |
subject_id, assay,
n_samples |
| Term | Definition |
|---|---|
| Analysis registry | A named set of AnalysisSpec objects that document the
analyses run on a cohort. Each spec has a unique name and describes its
input, method, and output. Stored in cohort@registry. |
| AnalysisSpec | An S7 object that documents one analysis: its name, description, input and output type, version, and any other configuration. Used to track how a result was produced. |
| Analysis artifact | An output of an analysis: a table, a plot, a model, or any other
object. Stored in cohort@analyses under the analysis name,
and read back later. |
| Term | Definition |
|---|---|
| Manifest | A CSV, or other tabular file, with the metadata and sample IDs for a
study. validate_manifest() and read_manifest()
turn it into subject_tbl and sample_map. |
| Manifest CSV | A long-format, comma-separated file, one row per sample. Required
columns: subject_id, assay,
sample_id. Optional: role, plus any
subject-level metadata (species, sex, genotype, cohort), which must stay
constant within a subject. |
| Term | Definition |
|---|---|
| Genotype | The genetic background of a subject, for example “WT” (wild-type), “KO” (knockout), or “HET” (heterozygous). Optional. |
| Sex | The biological sex of a subject: “M” or “F”. Optional. |
| Strain | The inbred strain or breed of a subject, for example “Fischer 344” or “B6”. Optional. |
| Cohort (column) | A treatment group or condition, for example “Control” or
“Treatment_A”. A subject-level column, distinct from a
Cohort object. |
| Timepoint | A study visit, age, or collection date, for example “Day 0” or “Week 12”. Optional. |
| Term | Definition |
|---|---|
| S7 class | R’s formal object system (the S7 package). It gives typed, immutable
properties and method dispatch. Study,
Subject, and Cohort are all S7 classes. |
| Property | A named field on an S7 object, read with @, for example
cohort@subject_tbl or study@title. Set once,
at construction. |
| Subject object | One subject’s metadata as an S7 object. Built on demand from a
cohort with subject(cohort, id), or directly with
subject_new(). A cohort stores subjects as rows of
subject_tbl, not as objects. |
| Cohort object | The main data container: subjects, sample mappings, optional study context, file paths, analyses, and a registry of analysis specs. |
| Term | Definition |
|---|---|
| Paths | A named list in cohort@paths that maps a name, for
example "wes_vcf_dir", to a file path or URL. Used to point
at analysis inputs and outputs. |
See Naming conventions for the standard names for columns, objects, and files.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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