S7 Subject class

An immutable S7 class for storing individual-level metadata in cross-species genomics studies. Subject objects represent individual animals or biological samples and are grouped into Cohort objects for collective analysis.

Usage

Subject(
  subject_id = character(0),
  species = character(0),
  sex = NA_character_,
  strain = NA_character_,
  genotype = NA_character_,
  cohort = NA_character_,
  timepoint = NA_character_,
  notes = NA_character_
)

Arguments

subject_id

Character scalar for unique subject identifier.

species

Character scalar naming the species. Any value is allowed; subject_new() stores it lower-cased.

sex

Character scalar for biological sex (e.g., "M", "F"). Optional.

strain

Character scalar for strain or breed designation. Optional.

genotype

Character scalar for genetic background or modification (e.g., "WT", "KO"). Optional.

cohort

Character scalar for cohort membership or treatment group. Optional.

timepoint

Character scalar for study timepoint or collection date. Optional.

notes

Character scalar for free-form annotations. Optional.

Value

A Subject object with the given properties.

Details

Use subject_new() to construct Subject objects; it lower-cases species. Construction also validates that subject_id and species are present, so building a Subject any other way still enforces the two required fields. Individual subjects are typically read from a Cohort with subject().

Access properties via the @ operator:

subject@subject_id
subject@species
subject@sex
subject@strain
subject@genotype
subject@cohort
subject@timepoint
subject@notes

See also

subject_new() for object construction, Cohort for managing groups of subjects

Examples

# The raw constructor; subject_new() is the usual way in.
rat <- Subject(subject_id = "R1", species = "rat", sex = "F")
rat@species
#> [1] "rat"
rat@genotype # NA until set
#> [1] NA