Documentation for SLiM function outputVCFSample, which is a method of the
SLiM class Subpopulation.
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.
outputVCFSample(
sampleSize,
replace,
requestedSex,
outputMultiallelics,
filePath,
append,
simplifyNucleotides,
outputNonnucleotides
)An object of type integer. Must be of length 1 (a singleton). 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 string. Must be of length 1 (a singleton).
The default value is "*". 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 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 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 741.
Output a random sample from the subpopulation in VCF format (see sections 27.2.3 and 27.2.4 for output format details). A sample of individuals (not genomes, note - unlike the outputSample() and outputMSSample() methods) of size sampleSize from the subpopulation will be output. The sample may be done either with or without replacement, as specified by replace; the default is to sample with replacement. A particular sex of individuals may be requested for the sample, for simulations in which sex is enabled, by passing "M" or "F" for requestedSex; passing "*", the default, indicates that genomes from individuals should be selected randomly, without respect to sex. If the sampling options provided by this method are not adequate, see the outputVCF() method of Genome for a more flexible low-level option. If the optional parameter filePath is NULL (the default), output will be sent to Eidos's output stream (see section 4.2.1). Otherwise, output will be sent to the filesystem path 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 outputMSSample() and outputSample() 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 Subpopulation:
Subpopulation,
addCloned(),
addCrossed(),
addEmpty(),
addRecombinant(),
addSelfed(),
addSpatialMap(),
cachedFitness(),
configureDisplay(),
defineSpatialMap(),
outputMSSample(),
outputSample(),
pointDeviated(),
pointInBounds(),
pointPeriodic(),
pointReflected(),
pointStopped(),
pointUniform(),
removeSpatialMap(),
removeSubpopulation(),
sampleIndividuals(),
setCloningRate(),
setMigrationRates(),
setSelfingRate(),
setSexRatio(),
setSpatialBounds(),
setSubpopulationSize(),
spatialMapColor(),
spatialMapImage(),
spatialMapValue(),
subsetIndividuals(),
takeMigrants()