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Write a BayeScan file from a tidy data frame

Source: R/write_bayescan.R
write_bayescan.Rd

Write a BayeScan file from a tidy data frame. The data is bi- or multi-allelic. Used internally in genometranslator and might be of interest for users.

Usage

write_bayescan(
  data,
  pop.select = NULL,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1,
  verbose = TRUE,
  ...
)

Arguments

data

A GDS file, open GDS object, tidy data frame object, or a tidy data frame in wide or long format in the working directory. For GDS input, individual metadata stored in the GDS supplies the codeSTRATA column. How to get a tidy data frame ? Look into genometranslator tidy_genome.

pop.select

(optional, string) Selected list of populations for the analysis. e.g. pop.select = c("QUE", "ONT") to select QUE and ONT population samples (out of 20 pops). If pop.labels argument was used to rename the strata column, use the new names with pop.select. Default: pop.select = NULL.

filename

(optional) The file name prefix for the bayescan file written to the working directory. With default: filename = NULL, the date and time is appended to genometranslator_bayescan_. Default: filename = NULL.

parallel.core

Number of workers available for parallel operations. Default: parallel.core = parallel::detectCores() - 1.

verbose

Logical indicating whether progress messages are emitted. Default: verbose = TRUE.

Value

A bayescan file is written in the working directory.

Details

BayeScan input should contain polymorphic markers represented in every selected stratum. Missingness, minor-allele thresholds, linkage disequilibrium, and other quality-control decisions should be addressed by the user before calling this writer. The function validates common-marker representation and polymorphism, but does not remove failing markers.

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.

Dependencies

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.

References

Foll, M and OE Gaggiotti (2008) A genome scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics 180: 977-993

Foll M, Fischer MC, Heckel G and L Excoffier (2010) Estimating population structure from AFLP amplification intensity. Molecular Ecology 19: 4638-4647

Fischer MC, Foll M, Excoffier L and G Heckel (2011) Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis). Molecular Ecology 20: 1450-1462

Author

Thierry Gosselin thierrygosselin@icloud.com