Cohort Objects for Subjects and Samples in Omics Studies

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Documentation for package ‘biocohort’ version 0.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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biocohort-package	biocohort: Subject and Sample Rosters for Omics Studies
AnalysisSpec	S7 AnalysisSpec class
analysis_files	Retrieve analysis file manifests from a cohort
analysis_list	List registered analysis specifications
analysis_register	Register an analysis specification in a cohort
analysis_spec	Retrieve an analysis specification from registry
analysis_spec_new	Create an AnalysisSpec object
apply_corrections	Apply documented corrections to a manifest
as_coldata	Build sample metadata for a count matrix
biocohort	biocohort: Subject and Sample Rosters for Omics Studies
check_paths	Check that a cohort's file paths exist on disk
Cohort	S7 Cohort class
cohort_contrasts	Every pairwise contrast between a cohort's groups
cohort_derive	Derive a column from cutoffs on an existing numeric column
cohort_filter	Keep a subset of a cohort's subjects or assays
cohort_groups	Group a cohort's subjects by one or more columns
cohort_new	Create a Cohort object
cohort_qc	Flag or drop subjects or samples for quality control
cohort_read	Read a cohort saved with cohort_save()
cohort_save	Save a cohort to an RDS file
completeness	Per-assay sample counts for a cohort
corrections_log	Return the audit table of a corrected manifest
derive_log	Read a cohort's derived-column log
ensure_dir	Create a folder when it is absent
example_cohort	Example Cohort Dataset
join_metadata	Add cohort metadata to an analysis object
liftover_backends	List registered liftover backends
liftover_crossmap	Liftover backend backed by CrossMap
liftover_intervals	Liftover a set of genomic intervals across assemblies or species
liftover_rtracklayer	Liftover backend backed by rtracklayer
liftover_vcf	Liftover a VCF of variants with CrossMap (allele-aware)
load_analyses	Load registered analyses into a cohort from disk
load_analysis	Load an analysis's feature table from disk
manifest_from_wide	Reshape a wide sample table into a long-format manifest
orthologize	Deprecated alias for translate()
ortholog_babelgene	Ortholog backend backed by babelgene
ortholog_backends	List registered ortholog backends
ortholog_genes	Map gene-level features to orthologs in another species
project_path	Build a path under the project root
project_root	Find the project root folder
qc_log	Read a cohort's QC log
read_corrections	Read a corrections table from a file
read_dotenv	Read a dotenv file into the environment
read_manifest	Read and validate a long-format manifest file
read_manifest_csv	Read and validate a long-format manifest CSV file
read_study_yaml	Build a cohort from a study YAML file
register_liftover_backend	Register a liftover backend
register_ortholog_backend	Register a gene-ortholog backend
samples	Read the sample map of a cohort
sample_pairs	Derive sample pairs from a sample map
sample_sheet	Write a pipeline sample sheet from a cohort
sample_sheet_templates	List the built-in sample sheet templates
Study	S7 Study class
study_new	Create a Study object
Subject	S7 Subject class
subject	Build one Subject from a cohort
subjects	Read the subject table of a cohort
subject_new	Create a Subject object
translate	Translate features (or a whole cohort) across species or assemblies
TranslationResult	Result of a cross-species or cross-assembly translation
translation_report	Retrieve per-analysis translation results from a cohort
translation_stats	Summary statistics for a translation
validate_cohort	Validate a Cohort object
validate_manifest	Validate and structure a long-format sample manifest
write_manifest	Write a manifest or a cohort's tables to a delimited file
write_study_yaml	Write a cohort as a study YAML file