Write data in rubias format

Convert a supported genomic dataset to the diploid, two-column-per-locus data frame used by rubias. The first four columns are sample_type, repunit, collection, and indiv.

Usage

write_rubias(
  data,
  strata = NULL,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1,
  verbose = TRUE
)

Arguments

data: A GDS file or object, or another genomic object accepted by read_genome().
strata: Optional sample metadata accepted by read_strata(). Supply SAMPLE_TYPE, REPUNIT, COLLECTION, and INDIVIDUALS for full control. Lower-case rubias names are also accepted. When these fields are absent, STRATA or POP_ID is used for both repunit and collection, and all samples are treated as references. Default: strata = NULL.
filename: Optional filename prefix. When supplied, the result is written as <filename>_rubias.tsv; a timestamp is added rather than overwriting an existing file. Default: filename = NULL.
parallel.core: Number of workers available while importing or transforming supported inputs. Retained for consistency with other writers. Default: parallel.core = parallel::detectCores() - 1.
verbose: Logical. Display progress messages. Default: verbose = TRUE.

Value

A tibble compatible with rubias. When filename is supplied, the same table is also written as a tab-separated file.

Details

rubias requires one row per diploid individual and four leading character columns:

sample_type must be "reference" or "mixture";
reference samples require non-missing repunit and collection;
mixture samples require repunit = NA, while collection identifies the mixture sample, port, stratum, place, or time group;
indiv must uniquely identify every individual.

Missing genotypes are written as two NA alleles. Partial diploid genotypes are rejected. Locus names cannot contain spaces because rubias uses adjacent columns to identify gene copies.

This writer creates an input representation; it does not run the conditional GSI model and does not silently filter individuals or loci. Quality control, marker selection, reference design, and the distinction between reference and mixture samples remain the user's responsibility.

Dependencies

The output schema follows the documented interface of rubias, developed by Eric C. Anderson and Ben Moran. Installing rubias is not required to create the table, but is required to analyse it. This implementation is independently written from the public input specification; no rubias source code is incorporated.

Required package dependencies are declared in DESCRIPTION and are installed with genometranslator. Any additional dependency needed only for this format or option is identified in this help page. Use genometranslator_dependencies() to inspect the availability of core packages, optional packages, and external executables.

Data filtering

This writer does not silently filter markers or individuals. It may validate requirements imposed by the destination format and stop with an informative error when the input is unsuitable. It is the user's responsibility to filter and quality-control the data appropriately for the intended analysis before generating the output. Use radr or another suitable workflow when filtering is required.

References

Moran BM, Anderson EC (2019). Bayesian inference from the conditional genetic stock identification model. Canadian Journal of Fisheries and Aquatic Sciences, 76(4), 551-560. doi:10.1139/cjfas-2018-0016 .