Documentation for SLiM function outputVCF, which is a method of the SLiM
class Genome.
Note that the R function is a stub, it does not do anything in R (except bring
up this documentation). It will only do
anything useful when used inside a slim_block function further
nested in a slim_script
function call, where it will be translated into valid SLiM code as part of a
full SLiM script.
outputVCF(
filePath,
outputMultiallelics,
append,
simplifyNucleotides,
outputNonnucleotides
)An object of type null or string. Must be of length 1 (a
singleton). The default value is NULL. See details for description.
An object of type logical. Must be of length 1 (a
singleton). The default value is T. See details for description.
An object of type logical. Must be of length 1 (a singleton). The
default value is F. See details for description.
An object of type logical. Must be of length 1 (a
singleton). The default value is F. See details for description.
An object of type logical. Must be of length 1 (a
singleton). The default value is T. See details for description.
An object of type void.
Documentation for this function can be found in the official SLiM manual: page 674.
Output the target genomes in VCF format (see sections 27.2.3, 27.2.4, and 27.3.3 for output format details). The target genomes are treated as pairs comprising individuals for purposes of structuring the VCF output, so an even number of genomes is required. This low-level output method may be used to output any sample of Genome objects (the Eidos function sample() may be useful for constructing custom samples, as may the SLiM class Individual). For output of a sample from a single Subpopulation, the outputVCFSample() of Subpopulation may be more straightforward to use. If the optional parameter filePath is NULL (the default), output is directed to SLiM's standard output. Otherwise, the output is sent to the file specified by filePath, overwriting that file if append if F, or appending to the end of it if append is T. The parameters outputMultiallelics, simplifyNucleotides, and outputNonnucleotides affect the format of the output produced; see sections 27.2.3 and 27.2.4 for further discussion. See outputMS() and output() for other output formats. Output is generally done in a late() event, so that the output reflects the state of the simulation at the end of a tick.
This is documentation for a function in the SLiM software, and has been reproduced from the official manual, which can be found here: http://benhaller.com/slim/SLiM_Manual.pdf. This documentation is Copyright © 2016-2020 Philipp Messer. All rights reserved. More information about SLiM can be found on the official website: https://messerlab.org/slim/
Other Genome:
Genome,
addMutations(),
addNewDrawnMutation(),
addNewMutation(),
containsMarkerMutation(),
containsMutations(),
countOfMutationsOfType(),
mutationCountsInGenomes(),
mutationFrequenciesInGenomes(),
mutationsOfType(),
nucleotides(),
outputMS(),
output(),
positionsOfMutationsOfType(),
readFromMS(),
readFromVCF(),
removeMutations(),
sumOfMutationsOfType()