Package index • biocohort

Package

Package overview and entry point

biocohort biocohort-package: biocohort: Subject and Sample Rosters for Omics Studies

Core Classes

S7 classes for study data structures

Study(): S7 Study class
Subject(): S7 Subject class
Cohort(): S7 Cohort class
AnalysisSpec(): S7 AnalysisSpec class
example_cohort: Example Cohort Dataset

Constructors

Create and validate objects

study_new(): Create a Study object
subject_new(): Create a Subject object
cohort_new(): Create a Cohort object
analysis_spec_new(): Create an AnalysisSpec object

Accessors

Read parts of a cohort

subject(): Build one Subject from a cohort
subjects(): Read the subject table of a cohort
samples(): Read the sample map of a cohort
completeness(): Per-assay sample counts for a cohort
cohort_filter(): Keep a subset of a cohort's subjects or assays

Quality control

Flag or drop subjects or samples, with an audit trail

cohort_qc(): Flag or drop subjects or samples for quality control
qc_log(): Read a cohort's QC log

Groups and contrasts

Group subjects and enumerate pairwise comparisons

cohort_groups(): Group a cohort's subjects by one or more columns
cohort_contrasts(): Every pairwise contrast between a cohort's groups

Derived columns

Bin a numeric column at named cutoffs, with provenance

cohort_derive(): Derive a column from cutoffs on an existing numeric column
derive_log(): Read a cohort's derived-column log

IO Functions

Read and write data

read_manifest(): Read and validate a long-format manifest file
read_manifest_csv(): Read and validate a long-format manifest CSV file
manifest_from_wide(): Reshape a wide sample table into a long-format manifest
write_manifest(): Write a manifest or a cohort's tables to a delimited file
cohort_save(): Save a cohort to an RDS file
cohort_read(): Read a cohort saved with cohort_save()

Analysis Registry

Register and list analyses

analysis_register(): Register an analysis specification in a cohort
analysis_list(): List registered analysis specifications
analysis_spec(): Retrieve an analysis specification from registry

Validation

Data validation functions

validate_manifest(): Validate and structure a long-format sample manifest
validate_cohort(): Validate a Cohort object

Samples

Work with the sample map

sample_pairs(): Derive sample pairs from a sample map

Pipeline sample sheets

Write the sample sheet a pipeline expects, and check its file paths

sample_sheet(): Write a pipeline sample sheet from a cohort
sample_sheet_templates(): List the built-in sample sheet templates
check_paths(): Check that a cohort's file paths exist on disk

Analysis loading

Read analysis feature tables from disk (experimental)

load_analysis(): Load an analysis's feature table from disk
load_analyses(): Load registered analyses into a cohort from disk
analysis_files(): Retrieve analysis file manifests from a cohort

Bridges

Carry cohort metadata into other analysis objects

as_coldata(): Build sample metadata for a count matrix
join_metadata(): Add cohort metadata to an analysis object

Cross-species translation

Translate features across assemblies and species (experimental)

translate(): Translate features (or a whole cohort) across species or assemblies
orthologize(): Deprecated alias for translate()
liftover_intervals(): Liftover a set of genomic intervals across assemblies or species
liftover_vcf(): Liftover a VCF of variants with CrossMap (allele-aware)
liftover_rtracklayer(): Liftover backend backed by rtracklayer
liftover_crossmap(): Liftover backend backed by CrossMap
register_liftover_backend(): Register a liftover backend
liftover_backends(): List registered liftover backends
ortholog_genes(): Map gene-level features to orthologs in another species
ortholog_babelgene(): Ortholog backend backed by babelgene
register_ortholog_backend(): Register a gene-ortholog backend
ortholog_backends(): List registered ortholog backends
translation_report(): Retrieve per-analysis translation results from a cohort
TranslationResult(): Result of a cross-species or cross-assembly translation
translation_stats(): Summary statistics for a translation

Project paths

Find the project root, build paths under it, and read a dotenv file

project_root(): Find the project root folder
project_path(): Build a path under the project root
ensure_dir(): Create a folder when it is absent
read_dotenv(): Read a dotenv file into the environment

Corrections

Apply documented overrides to a manifest and keep an audit trail

apply_corrections(): Apply documented corrections to a manifest
corrections_log(): Return the audit table of a corrected manifest
read_corrections(): Read a corrections table from a file

Study configuration

Declare a study, its manifest, and its analyses in one YAML file

read_study_yaml(): Build a cohort from a study YAML file
write_study_yaml(): Write a cohort as a study YAML file