Write a rubias object

Source: R/write_rubias.R

Write a rubias object from a tidy data frame or GDS file/object.

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

Arguments

data

(4 options) A file or object generated by radiator:

  • tidy data

  • Genomic Data Structure (GDS)

How to get GDS and tidy data ? Look into tidy_genomic_data, read_vcf or tidy_vcf.

strata

(optional, tibble file or object) This tibble of individual's metadata must contain four columns: SAMPLE_TYPE, REPUNIT, COLLECTION, INDIVIDUALS. Those columns are described in rubias. Default:strata = NULL. With default, SAMPLE_TYPE is filled with reference. REPUNIT and COLLECTION will be filled by the STRATA or POP_ID column found in the data.

filename

The prefix for the name of the file written to the working directory. Default: filename = NULL. With default, only the rubias object is generated. The filename will be appended _rubias.tsv.

parallel.core

(optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

Value

A rubias object in the global environment and a file is written in the working directory if filename argument was used.

References

Moran BM, and Anderson, E. C. 2018 Bayesian inference from the conditional genetic stock identification model. Can. J. Fish. Aquat. Sci. 76: 551-560.

Anderson, Eric C., Robin S. Waples, and Steven T. Kalinowski. (2008) An improved method for predicting the accuracy of genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences 65, 7:1475-1486.

Anderson, E. C. (2010) Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased. Molecular ecology resources 10, 4:701-710.

See also

/hrefhttps://github.com/eriqande/rubiasrubias: genetic stock identification (GSI) in the tidyverse.

Author

Thierry Gosselin thierrygosselin@icloud.com