Write a COLONY input file — write_colony • genometranslator

Write a COLONY input file.

Usage

write_colony(
  data,
  strata = NULL,
  sample.markers = NULL,
  pop.select = NULL,
  allele.freq = NULL,
  inbreeding = 0,
  mating.sys.males = 0,
  mating.sys.females = 0,
  clone = 0,
  run.length = 2,
  analysis = 1,
  allelic.dropout = 0,
  error.rate = 0.02,
  print.all.colony.opt = FALSE,
  random.seed = NULL,
  verbose = FALSE,
  parallel.core = parallel::detectCores() - 1,
  filename = NULL,
  ...
)

Arguments

data

A supported genomic file, object, or tidy genomic data frame. Default: data = NULL.

strata

(path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available. Default: strata = NULL.

sample.markers

(number) COLONY can take a long time to run, use a random subsample of your markers to speed test COLONY e.g. sample.markers = 500 to use only 500 randomly chosen markers. With the default, Will use all markers. Default: sample.markers = NULL.

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.

allele.freq

(optional, string) Allele frequency can be computed from a select group. e.g. allele.freq = "QUE" or allele.freq = c("QUE", "ONT"). Using allele.freq = "overall" will use all the samples to compute the allele frequency. With the default, Will not compute allele frequency. Default: allele.freq = NULL.

inbreeding

(boolean) 0/1 no inbreeding/inbreeding. Default: inbreeding = 0.

mating.sys.males

(boolean) Mating system in males. 0/1 polygyny/monogyny. Default: mating.sys.males = 0.

mating.sys.females

(boolean) Mating system in females. 0/1 polygyny/monogyny. Default: mating.sys.females = 0.

clone

(boolean) Should clones and duplicated individuals be inferred. 0/1, yes/no. Default: clone = 0.

run.length

(integer) Length of run. 1 (short), 2 (medium), 3 (long), 4 (very long). Start with short or medium run and consider longer run if your estimates probability are not stable or really good. Default: run.length = 2.

analysis

(integer) Analysis method. 0 (Pairwise-Likelihood Score), 1 (Full Likelihood), 2 (combined Pairwise-Likelihood Score and Full Likelihood). Default: analysis = 1.

allelic.dropout

Locus allelic dropout rate. Default : allelic.dropout = 0. Default: allelic.dropout = 0.

error.rate

Locus error rate. Default: error.rate = 0.02.

print.all.colony.opt

(logical) Should all COLONY options be printed in the file.

This require manual curation, for the file to work directly with COLONY. Default = print.all.colony.opt = FALSE. Default: print.all.colony.opt = FALSE.

random.seed

(integer, optional) For reproducibility, set an integer that will be used inside the function that requires randomness. With default, a random number is generated and printed in the appropriate output. Default: random.seed = NULL.

verbose

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

parallel.core

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

filename

Name of the acronym for filenaming in the working directory. Default: filename = NULL.

...

Additional arguments passed to lower-level readers, translators, or writers.

Value

A COLONY file in your working directory (2 if you selected imputations arguments...)

Details

It is highly recommended to read (twice!) the user guide distributed with COLONY to find out the details for input and output of the software.

Not all options are provided here.

But to ease the process, all the required options to properly run COLONY will be printed in the file written in your working directory. Change the values accordingly and wisely.

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

Jones OR, Wang J (2010) COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources, 10, 551–555.

Wang J (2012) Computationally Efficient Sibship and Parentage Assignment from Multilocus Marker Data. Genetics, 191, 183–194.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
# Simplest way to run the function with a tidy dataset:
colony.file <- genometranslator::write_colony(data = "turtle.data.rad")
} # }

Write a `COLONY` input file