Rsampletrees (version 1.0.3)

changeArgs.treeoutput: Modify the settings stored in a sampletrees treeoutput object

Description

Modify the settings stored in a sampletrees treeoutput object.

Usage

# S3 method for treeoutput
changeArgs(object,...)

Arguments

object

An object of class `treeoutput'

…

Optional tag names and the value they should be set to. See Details section.

Value

Returns an object of class `treeoutput' with the runinfo settings modified as specified.

The settings names in the runinfo component are:

RunName

Run name for the sampletrees run (Default="Run")

Seed

Initial seed for sampletrees run. (Default=NA)

DataType

The type of the data file g=genotype h=haplotype. (Default="h")

DataFile

The name of the file containing the haplotype or genotype data. DEFAULT=NA but the user must change this value before running sampletrees()

LocationFile

The name of the file containing the genomic locations (in base pairs) of the SNP markers. Default=NA but the user must change this value before running sampletrees()

WeightFile

The name of the file containing the probabilities for sampling each of the 7 updates. Default=NA but the user must change this value before running sampletrees(). See setWeights for more information.

FocalPoint

The location of the focal point. Default=NA but the user must change this value before running sampletrees()

ChainLength

How long to run the chain. (Default=1000)

BurnIn

Discard the first 'BurnIn' samples. (Default=100)

Thinning

Return output every 'Thinning'th sample. (Default=1)

InitialTheta

Initial value for mutation rate theta. (Default=1)

MinTheta

Minimum for Uniform prior for theta. (Default=0.0001)

MaxTheta

Maximum for Univorm prior for theta. (Default=10)

InitialRho

Initial value for recombination rate rho. (Default=0.0004)

ScaleRho

Scale parameter for gamma prior for rho. (Default=0.1)

ShapeRho

Shape parameter for gamma prior for rho. (Default=1)

InitialTreeFile

Name for a file containing initial tree data for a run of sampletrees. These are typically available from a previous run of sampletrees. If DataType="g", initial haplotype configurations will be taken from this file rather than one specified by InitialHaploFile. (Default=NA)

RandomTree

Indicates whether initial tree generated by randomly connecting nodes. (Default=FALSE)

HaploFreqFile

The name of the file with the haplo frequency estimates to be used only if DataType="g". See estimateHapFreqs() for more information. Default=NA but user must change this value if DataType is 'g'.

InitialHaploFile

Name for an optional file containing the initial haplotype configurations for the sampletrees run (optional if DataType="g"). Each row of this file corresponds to a haplotype, there are 2 rows/individual and rows must be in the same order as in DataFile. (Default=NA)

HaploListFile

Name for a optional file containing a list of likely haplotypes (optional if DataType="g"). Each row corresponds to a haplotype. (Default=NA)

Details

The function changeArgs modifies the settings values from a run of sampletrees (the settings are stored in the runinfo component of the treeoutput object). The format for passing arguments to this function is: TagName=Value. The names are given in the Value section.

References

Burkett KM, McNeney B, Graham J. Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data. Bioinformatics. 32:1580-2, 2016

See Also

changeArgs.pars, checkArgs

Examples

# NOT RUN {
#\dontrun{
 #system.file("Examples/example_g_pars",package="Rsampletrees")
filename=paste(path.package("Rsampletrees"),"/extdata/example_g_pars",sep="")
runpars=readArgs(filename, check=FALSE)
#paste(system.file(package="Rsampletrees"),runpars$RunName, sep="/")
runname=paste(path.package("Rsampletrees"),"extdata",runpars$RunName, sep="/")
runpars=changeArgs(runpars, RunName=runname)
results=readOutput(argobj=runpars)
results=changeArgs(results, RunName="NewName")
#}
# }