Write a cohort as a study YAML file

The inverse of read_study_yaml(): writes the cohort's study metadata, its manifest, its paths, and its registered analysis specs to a study YAML file and a manifest file alongside it.

Usage

write_study_yaml(cohort, path, manifest = "manifest.csv")

Arguments

cohort

A Cohort object.

path

Output path for the study YAML file.

manifest

Path for the manifest file, resolved relative to path's directory unless absolute. Default "manifest.csv".

Value

path, invisibly.

Details

A cohort has no stored corrections file, so a corrections: key is never written; the manifest written out already reflects any correction that was applied before the cohort was built.

See also

read_study_yaml(), write_manifest()

Examples

data(example_cohort)
dir <- tempfile()
dir.create(dir)
write_study_yaml(example_cohort, file.path(dir, "study.yaml"))
cat(readLines(file.path(dir, "study.yaml")), sep = "\n")
#> manifest: manifest.csv
#> study:
#>   study_id: STUDY001
#>   title: Cross-species genomics comparison
#>   description: Example study comparing rat and mouse genomes
#>   hypotheses:
#>   - Orthologous genes show conserved expression patterns
#>   - Species-specific variants drive phenotypic differences
#>   aims:
#>   - Map rat genes to mouse orthologs
#>   - Identify conserved regulatory regions
#>   assays:
#>   - WES
#>   - snRNA-seq
#>   genome_builds:
#>     rat: rn7
#>     mouse: mm10
#>     human: hg38
#> sample_cols:
#> - fastq_1
#> - fastq_2