Write a COLONY input file

Write a COLONY input file.

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

(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

(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.

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. Default: sample.markers = NULL, will use all markers.

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). 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. Default: allele.freq = NULL, will not compute allele frequency.

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.

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.

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

(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

parallel.core

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

filename

Name of the acronym for filenaming in the working directory.

...

(optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

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.

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.

See also

COLONY is available on Jinliang Wang web site https://www.zsl.org/science/software/colony

colony installation instructions

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

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