Write a BayeScan file from a tidy data frame. The data is bi- or multi-allelic. Used internally in radiator and might be of interest for users.
write_bayescan(
data,
pop.select = NULL,
filename = NULL,
parallel.core = parallel::detectCores() - 1,
...
)A tidy data frame object in the global environment or
a tidy data frame in wide or long format in the working directory.
How to get a tidy data frame ?
Look into radiator tidy_genomic_data.
(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).
Default: pop.select = NULL
(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 radiator_bayescan_.
(optional) The number of core used for parallel
execution during import.
Default: parallel.core = parallel::detectCores() - 1.
(optional) To pass further arguments for fine-tuning the function.
A bayescan file is written in the working directory.
Integrated filters:
by defaults only markers found in common between populations are used
by defaults monomorphic markers are automatically removed before generating the dataset.
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