S7 Study class

An immutable S7 class for storing project-level metadata for a study. Study objects provide high-level context and configuration for cohorts and analyses, for any organism and any omics assay.

Usage

Study(
  study_id = character(0),
  title = character(0),
  description = NA_character_,
  hypotheses = character(0),
  aims = character(0),
  assays = character(0),
  genome_builds = list(),
  created_at = Sys.time(),
  tags = character(0)
)

Arguments

study_id

Character scalar for study identifier. Unique within a project.

title

Character scalar for study name/title.

description

Character scalar for longer description of study purpose, design, or protocols. Optional.

hypotheses

Character vector of research hypotheses. Accepts multiple hypotheses. Optional.

aims

Character vector of specific research aims. Accepts multiple aims. Optional.

assays

Character vector of assay types used (e.g., "wes", "scrna"). Optional.

genome_builds

Named list mapping species to genome build versions, e.g. list(rat = "rn7", mouse = "mm39", human = "hg38"). Any species name and any build string are accepted. Optional.

created_at

POSIXct timestamp for creation. Defaults to the time the object is built.

tags

Character vector of arbitrary tags for categorization. Optional.

Value

A Study object with the given properties.

Details

Use study_new() to construct Study objects with immediate validation. Construction also validates study_id and title directly, so building a Study any other way still enforces the two required fields.

Access properties via the @ operator:

study@study_id
study@title
study@description
study@hypotheses
study@aims
study@assays
study@genome_builds
study@created_at
study@tags

See also

study_new() for object construction, Cohort for combining studies with subject data

Examples

# The raw constructor; study_new() is the usual way in.
study <- Study(study_id = "PILOT", title = "Pilot study")
study@study_id
#> [1] "PILOT"
study@assays # empty until set
#> character(0)