Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/post_sampletrees.R
Modify the settings stored in a sampletrees treeoutput object.
1 2 | ## S3 method for class 'treeoutput'
changeArgs(object,...)
|
object |
An object of class ‘treeoutput’ |
... |
Optional tag names and the value they should be set to. See Details section. |
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.
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) |
Kelly Burkett
Burkett KM, McNeney B, Graham J. Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data. Bioinformatics. 32:1580-2, 2016
changeArgs.pars, checkArgs
1 2 3 4 5 6 7 8 9 10 | #\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")
#}
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